Chimeric DNA-binding proteins

ABSTRACT

Chimeric proteins containing composite DNA-binding regions are disclosed together with DNA constructs encoding them, compositions containing them and applications in which they are useful.

RELATED APPLICATIONS

This application is a divisional of U.S. Ser. No. 11/369,889 filed Mar.7, 2006 now U.S. Pat. No. 7,485,441); which is a continuation of U.S.Ser. No. 09/852,370 filed May 10, 2001 (now U.S. Pat. No. 7,008,780)issue date Mar. 7, 2006; which is a divisional of U.S. Ser. No.08/973,131 filed Mar. 16, 1998 (now U.S. Pat. No. 6,326,166) issue dateDec. 4, 2001; which is a national stage entry of PCT/US95/16982 filedDec. 29, 1995 which is a continuation-in-part of U.S. Ser. No.08/366,083 filed Dec. 29, 1994 (now abandoned). The entire contents ofeach of these priority applications are hereby incorporated byreference.

GOVERNMENT SUPPORT

A portion of the work described herein was supported by grantsPO1-CA42063, CDR-8803014 and P30-CA14051 from the U.S. Public HealthService/National Institutes of Health, National Science Foundation andNational Cancer Institute, respectively. The U.S. Government has certainrights in the invention. A portion of the work described herein was alsosupported by the Howard Hughes Medical Institute.

SEQUENCE LISTING

Pursuant to 37 CFR 1.52(e)(5) the sequence listing filed herewith (ST25.txt, 22 kb, created on Dec. 10, 2008) is incorporated by reference.

BACKGROUND OF THE INVENTION

DNA-binding proteins, such as transcription factors, are criticalregulators of gene expression. For example, transcriptional regulatoryproteins are known to play a key role in cellular signal transductionpathways which convert extracellular signals into altered geneexpression (Curran and Franza, Cell 55:395-397 (1988)). DNA-bindingproteins also play critical roles in the control of cell growth and inthe expression of viral and bacterial genes. A large number ofbiological and clinical protocols, including among others, gene therapy,production of biological materials, and biological research, depend onthe ability to elicit specific and high-level expression of genesencoding RNAs or proteins of therapeutic, commercial, or experimentalvalue. Such gene expression is dependent on protein-DNA interactions.

Attempts have been made to change the specificity of DNA-bindingproteins. Those attempts rely primarily on strategies involvingmutagenesis of these proteins at sites important for DNA-recognition(Rebar and Pabo, Science 263:671-673 (1994), Jamieson et al.,Biochemistry 33:5689-5695 (1994), Suckow et al., Nucleic Acids Research22(12):2198-2208 (1994)). This strategy may not be efficient or possiblewith some DNA-binding domains because of limitations imposed by theirthree-dimensional structure and mode of docking to DNA. In other casesit may not be sufficient to achieve important objectives discussedbelow. Therefore, it is desirable to have a strategy which can utilizemany different DNA-binding domains and can combine them as required forDNA recognition and gene regulation.

SUMMARY OF THE INVENTION

This invention pertains to chimeric proteins which contain at least onecomposite DNA-binding region and possess novel nucleic acid bindingspecificities. The chimeric proteins recognize nucleotide sequences (DNAor RNA) spanning at least 10 bases and bind with high affinity tooligonucleotides or polynucleotides containing such sequences. (Itshould be understood that the nucleotide sequences recognized by thechimeric proteins may be RNA or DNA, although for the sake ofsimplicity, the proteins of this invention are typically referred to as“DNA-binding”, and RNA too is understood, if not necessarily mentioned.)

The terms “chimeric” protein and “composite” domain are used to denote aprotein or domain containing at least two component portions which aremutually heterologous in the sense that they do not occur together inthe same arrangement in nature. More specifically, the componentportions are not found in the same continuous polypeptide sequence ormolecule in nature, at least not in the same order or orientation orwith the same spacing present in the chimeric protein or compositedomain.

As discussed in detail below, a variety of component DNA-bindingpolypeptides known in the art are suitable for adaptation to thepractice of this invention. The chimeric proteins contain a compositeregion comprising two or more component DNA-binding domains, joinedtogether, either directly or through one amino acid or through a shortpolypeptide (two or more amino acids) to form a continuous polypeptide.Additional domains with desired properties can optionally be included inthe chimeric proteins. For example, a chimeric protein of this inventioncan contain a composite DNA-binding region comprising at least onehomeodomain, such as the Oct-1 homeodomain, together with a secondpolypeptide domain which does not occur in nature identically linked tothat homeodomain. Alternatively, the composite DNA-binding domain cancomprise one or more zinc finger domains such as zinc finger 1 and/orfinger 2 of Zif268, together with a second polypeptide domain which doesnot occur in nature linked to that zinc finger domain(s).

A number of specific examples examined in greater detail below involvechimeric proteins containing a composite DNA-binding region comprising ahomeodomain and one or two zinc finger domains. In one embodiment, thechimeric protein is a DNA-binding protein comprising at least onehomeodomain, a polypeptide linker and at least one zinc finger domain.Such a chimeric protein is exemplified by a composite DNA-binding regioncontaining zinc finger 1 or zinc finger 2 of Zif268, an amino acid or ashort (2-5 amino acid residue) polypeptide, and the Oct-1 homeodomain.Another example is a chimeric protein containing a composite DNA-bindingregion comprising zinc fingers 1 and 2 of Zif268, a short linker, suchas a glycine-glycine-arginine-arginine polypeptide, and the Oct-1homeodomain. The latter chimeric protein, designated ZFHD1, is describedin detail below. Other illustrative composite DNA-binding regionsinclude those comprising the Oct1 POU specific domain (aa 268-343) andits own flexible linker (aa 344-366) fused to the amino terminus ofZFHD1 and ZFHD1 fused at its carboxy terminus to Zif268 fingers 1 and 2(aa 333-390) via the Oct1 flexible linker.

In other embodiments, the chimeric protein comprises a compositeDNA-binding region containing a chimeric zincfinger-basic-helix-loop-helix protein. One such chimeric proteincomprises fingers 1 and 2 of Zif268 and the MyoD bHLH region, joined bya polypeptide linker which spans approximately 9.5 Å between thecarboxyl-terminal region of finger 2 and the amino-terminal region ofthe basic region of the bHLH domain.

In another embodiment, the chimeric protein comprises a compositeDNA-binding region containing a zinc finger-steroid receptor fusion. Onesuch chimeric protein comprises fingers 1 and 2 of Zif268 and theDNA-binding domains of the glucocorticoid receptor, joined at thecarboxyl-terminal region of finger 2 and the amino-terminal region ofthe DNA-binding domain of the glucocorticoid receptor by a polypeptidelinker which spans approximately 7.4 Å.

As will be seen, one may demonstrate experimentally the selectivity ofbinding of a chimeric protein of this invention for a recognized DNAsequence. One aspect of that specificity is that the chimeric protein iscapable of binding to its recognized nucleotide sequence preferentiallyover binding to constituent portions of that nucleotide sequence orbinding to different nucleotide sequences. In that sense, the chimericproteins display a DNA-binding specificity which is distinct from thatof each of the component DNA-binding domains alone; that is, they preferbinding the entire recognized nucleotide sequence over binding to a DNAsequence containing only a portion thereof. That specificity andselectivity means that the practitioner can design composite DNA-bindingregions incorporating DNA-binding domains of known nucleotide bindingspecificities with the knowledge that the composite protein willselectively bind to a corresponding composite nucleotide sequence andwill do so preferentially over the constituent nucleotide sequences.

These chimeric proteins selectively bind a nucleotide sequence, whichmay be DNA or RNA, spanning at least 10 bases, preferably at least 11bases, and more preferably 12 or more bases. By way of example, one canexperimentally demonstrate selective binding for a 12-base pairnucleotide sequence using the illustrative ZFHD1 composite DNA-bindingdomain. Typically one will obtain binding to the selected DNA sequencewith a Kd value of about 10⁻⁸ or better, preferably 10⁻⁹ or better andeven more preferably 10⁻¹⁰ or better. Kd values may be determined by anyconvenient method. In one such method one conducts a series ofconventional DNA binding assays, e.g. gel shift assays, varying theconcentration of DNA and determining the DNA concentration whichcorrelates to half-maximal protein binding.

The nucleotide sequence specificity of binding by chimeric proteins ofthis invention, illustrated by proteins comprising the peptide sequenceof ZFHD1, renders them useful in a number of important contexts becausetheir DNA-binding properties are distinct from those of known proteins.Such uses include the selective transcription, repression or inhibitionof transcription, marking, and cleavage of a target nucleotide sequence.The chimeric proteins prefer to bind to a specific nucleic acid sequenceand, thus, mark, cleave or alter expression of genes linked to orcontrolled by a nucleotide sequence containing the recognized nucleicacid sequence. Preferably, the chimeric proteins do not to a significantextent bind the DNA bound by the component domains of the compositeDNA-binding region, and, thus, do not mark, cleave or alter normalcellular gene expression other than by design.

In one application, the chimeric proteins bind a selected nucleic acidsequence within a DNA or RNA and, as a result, mark or flag the selectedDNA or RNA sequence, which can be identified and/or isolated from theDNA using known methods. In this respect, the chimeric proteins act in amanner similar to restriction enzymes, in that they recognize DNA or RNAat a selected nucleic acid sequence, thus marking that sequence whereever it occurs in DNA or RNA with which the chimeric proteins arecontacted. Unlike restriction enzymes, chimeric DNA-binding orRNA-binding proteins do not cut or fragment the DNA or RNA at thenucleic acids they recognize. Chimeric proteins used for this purposecan be labelled, e.g., radioactively or with an affinity ligand orepitope tag such as GST, and thus, the location of DNA or RNA to whichthey bind can be identified easily. Because of the binding specificityof the chimeric proteins, DNA or RNA to which binding occurs mustinclude either the nucleotide sequence which the chimeric proteins havebeen designed to recognize or the nucleotide sequences recognized by thecomponent DNA-binding domains. Optimally, the chimeric protein will notefficiently recognize the nucleotide sequence recognized by thecomponent DNA-binding domains. Standard methods, such as DNA cloning andsequencing, can be used to determine the nucleotide sequence to whichthe chimeric protein is bound.

In view of the ability of a composite DNA-binding region to fold andfunction in an autonomous manner, chimeric proteins of the variousembodiments of this invention may further comprise one or moreadditional domains, including for example a transcription activationdomain, a transcription repressing domain, a DNA-cleaving domain, aligand-binding domain, or a protein-binding domain.

Such a chimeric protein which contains a transcription activation domainconstitutes a chimeric transcription factor which is capable ofactivating the transcription of a gene linked to a DNA sequencerecognized (i.e., selectively bound) by the chimeric protein. Varioustranscription activation domains are known in the art and may be used inchimeric proteins of this invention, including the Herpes Simplex VirusVP16 activation domain and the NF-κB p65 activation domain which arederived from naturally occurring transcription factors. One class ofsuch transcription factors comprise at least one composite DNA-bindingregion, e.g. one containing at least one homeodomain and at least onezinc finger domain (such as the peptide sequence of ZFHD1), and at leastone additional domain capable of activating transcription of a genelinked to a DNA sequence to which the transcription factor can bind.These are illustrated by the ZFHD1-VP16 and ZFHD1-p65 chimeras discussedbelow.

Chimeric proteins of this invention also include those which are capableof repressing transcription of a target gene linked to a nucleotidesequence to which the chimeric proteins bind. Such a chimeric proteinfunctions as a somewhat classical repressor by binding to a nucleotidesequence and blocking, in whole or part, the otherwise normalfunctioning of that nucleotide sequence in gene expression, e.g. bindingto an endogenous transcription factor. Other chimeric proteins of thisinvention which are capable of repressing or inhibiting transcription ofa target gene linked to a nucleotide sequence to which the chimericprotein binds include chimeric proteins containing a compositeDNA-binding region, characteristic of all chimeric proteins of thisinvention, and an additional domain, such as a KRAB domain or assn-6/TUP-1 or Krüppel-family suppressor domain, capable of inhibitingor repressing the expression of the target gene in a cell. In eithercase, binding of the chimeric protein to the nucleotide sequence linkedto the target gene is associated with decreased transcription of thetarget gene.

Chimeric proteins of this invention also include those which are capableof cleaving a target DNA or RNA linked to a nucleotide sequence to whichthe chimeric proteins bind. Such chimeric proteins contain a compositeDNA-binding region, characteristic of all chimeric proteins of thisinvention, and an additional domain, such as a FokI domain, capable ofcleaving a nucleic acid molecule. Binding of the chimeric protein to therecognition sequence linked to the target DNA or RNA is associated withcleavage of the target DNA or RNA.

Chimeric proteins of this invention further include those which arecapable of binding to another protein molecule, e.g., for use inconducting otherwise conventional two-hybrid experiments. See e.g.,Fields and Song, U.S. Pat. No. 5,283,173 (Feb. 1, 1994). In addition tothe characteristic composite DNA-binding region, proteins of thisembodiment contain an additional domain which is, or may be, capable ofbinding to another protein, known or unknown. In such experiments, thechimeric protein containing the composite DNA-binding region replacesthe GALA-containing fusion protein in the 2-hybrid system and thenucleotide sequence recognized by our chimeric protein replaces the GALAbinding sites linked to the reporter gene.

Chimeric proteins of this invention further include those which furthercontain a ligand-binding domain permitting ligand-regulatedmanifestation of biological activity. Chimeric DNA-binding proteins ofthis aspect of the invention can be complexed or “dimerized” with otherligand-binding fusion proteins by the presence of an appropriatedimerizing ligand. Examples of such chimeric proteins include proteinscontaining a characteristic composite DNA-binding region and aligand-binding domain such as an immunophilin like FKBP12. The divalentligand, FK1012, for example, is capable of binding to a chimeric proteinof this invention which also contains one or more FKBP domains and toanother FKBP-containing protein, including a fusion protein containingone or more copies of FKBP linked to a transcription activation domain.See Spencer, D. M., et al. 1993. Science. 262:1019-1024, andPCT/US94/01617. Cells expressing such fusion proteins are capable ofdimerizer-dependent transcription of a target gene linked to anucleotide sequence to which the DNA-binding chimera is capable ofbinding.

This invention further encompasses DNA sequences encoding the chimericproteins containing a composite DNA-binding region. Such DNA sequencesinclude, among others, those which encode a chimeric protein in whichthe composite DNA-binding region contains a homeodomain covalentlylinked to at least one zinc finger domain, exemplified by chimericproteins containing the peptide sequence of ZFHD1. As should be clearfrom the preceding discussion, the DNA sequence may encode a chimericprotein which further comprises one or more additional domainsincluding, for instance, a transcription activation domain, atranscription repressing domain, a domain capable of cleaving anoligonucleotide or polynucleotide, a domain capable of binding toanother protein, a ligand-binding domain or a domain useful as adetectable label.

This invention further encompasses a eukaryotic expression constructcontaining a DNA sequence encoding the chimeric protein operably linkedto expression control elements such as promoter and enhancer elementspermitting expression of the DNA sequence and production of the chimericprotein in eukaryotic cells. One or more of those expression controlelements may be inducible, permitting regulated expression of the DNAencoding the chimeric protein. The expression control elements may betissue-specific or cell-type-specific, permitting preferential orselective expression of the chimeric protein in a cell-type or tissue ofparticular interest. An example of a eukaryotic expression vector ofthis invention is the plasmid pCGNN ZFHD1-FKBPX3 (ATCC No. 97399) whichis capable of directing the expression in mammalian cells of a fusionprotein containing a ZFHD1 composite DNA-binding region linked to threeFKBP12 domains, discussed in greater detail below.

Using DNA sequences encoding the chimeric proteins of this invention,and vectors capable of directing their expression in eukaryotic cells,one may genetically engineer cells for a number of important uses. To doso, one first provides an expression vector or construct for directingthe expression in a eukaryotic cell of the desired chimeric protein andthen introduces the vector DNA into the cells in a manner permittingexpression of the introduced DNA in at least a portion of the cells. Onemay use any of the various methods and materials for introducing DNAinto cells for heterologous gene expression, many of which are wellknown. A variety of such materials are commercially available.

In some cases the target gene and its linked nucleotide sequencespecifically recognized by the chimeric protein are endogenous to, orotherwise already present in, the engineered cells. In other cases, DNAcomprising the target gene and/or the recognized DNA sequence is notendogenous to the cells and is also introduced into the cells.

The various DNA constructs may be introduced into cells maintained inculture or may be administered to whole organisms, including humans andother animals, for introduction into cells in vivo. A variety of methodsand materials to effect the delivery of DNA into animals for theintroduction into cells are known in the art.

By these methods, one may genetically engineer cells, whether in cultureor in vivo, to express a chimeric protein capable of binding to a DNAsequence linked to a target gene within the cells and marking the DNAsequence, activating transcription of the target gene, repressingtranscription of the target gene, cleaving the target gene, etc.Expression of the chimeric protein may be inducible, cell-type-specific,etc., and the biological effect of the chimeric protein may beligand-dependent, all as previously mentioned.

This invention further encompasses genetically engineered cellscontaining and/or expressing any of the constructs described herein,particularly a construct encoding a protein comprising a compositeDNA-binding region, including prokaryotic and eucaryotic cells and inparticular, yeast, worm, insect, mouse or other rodent, and othermammalian cells, including human cells, of various types and lineages,whether frozen or in active growth, whether in culture or in a wholeorganism containing them. Several examples of such engineered cells areprovided in the Examples which follow. Those cells may further contain aDNA sequence to which the encoded chimeric protein is capable ofbinding. Likewise, this invention encompasses any non-human organismcontaining such genetically engineered cells. To illustrate this aspectof the invention, an example is provided of a mouse containingengineered cells expressing, in a ligand-dependent manner, an introducedtarget gene linked to a nucleotide sequence recognized by a chimericprotein containing a composite DNA-binding region.

The foregoing materials and methods permit one to mark a DNA sequencerecognized by the chimeric protein as well as to actuate or inhibit theexpression of target gene or to cleave the target gene. To do so, onefirst provides cells containing and capable of expressing a first DNAsequence encoding a chimeric protein which is capable of binding to asecond DNA sequence linked to a target gene of interest also presentwithin the cells. The chimeric protein is chosen for its ability to bindto and mark, cleave, actuate or inhibit transcription of, etc. thetarget gene. The cells are then maintained under conditions permittinggene expression and protein production. Again, gene expression may beinducible or cell-type specific, and the cells may be maintained inculture or within a host organism.

This invention may be applied to virtually any use for which recognitionof specific nucleic acid sequences is critical. For instance, thepresent invention is useful for gene regulation; that is, the novelDNA-binding chimeric proteins can be used for specific activation orrepression of transcription of introduced or endogenous genes to controlthe production of their gene products, whether in cell culture or inwhole organisms. In the context of gene therapy, it may be used tocorrect or compensate for abnormal gene expression, control theexpression of disease-causing gene products, direct the expression of aproduct of a naturally occurring or engineered protein or RNA oftherapeutic or prophylactic value, or to otherwise modify the phenotypeof cells introduced into or present within an organism, includingmammalian subjects, and in particular including human patients. Forinstance, the invention may be used in gene therapy to increase theexpression of a deficient gene product or decrease expression of aproduct which is overproduced or overactive. This invention may also beused to control gene expression in a transgenic organism for proteinproduction.

The chimeric proteins of the present invention can also be used toidentify specific rare DNA sequences, e.g., for use as markers in genemapping. To identify a DNA sequence in a mixture, one provides a mixturecontaining one or more DNA sequences; contacts the mixture with achimeric protein of this invention under conditions permitting thespecific binding of a DNA-binding protein to a recognized DNA sequence;and, determines the occurrence, amount and/or location of any DNAbinding by the chimeric protein. For example, the chimeric protein maybe labeled with a detectable label or with a moiety permitting recoveryfrom the mixture of the chimeric protein with any bound DNA. Using suchmaterials, one may separately recover the chimeric protein and an boundDNA from the mixture and isolate the bound DNA from the protein ifdesired.

Also, embodiments involving chimeric proteins containing a domaincapable of cleaving DNA provide a new series of sequence-specificendonuclease proteins. Chimeric DNA-binding proteins of the presentinvention can also be used to induce or stabilize loop formation in DNAor to bring together or hold together DNA sites on two or more differentmolecules.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-C illustrates selection by ZFHD1 of a hybrid binding site from apool of random oligonucleotides. FIG. 1A is a graphic representation ofthe structure of the ZFHD1 chimeric protein used to select binding sites(SEQ ID NO: 75). The underlined residues are from the Zif268-DNA andOct-1-DNA crystal structures and correspond to the termini used incomputer modeling studies. The linker contains two glycines, which wereincluded for flexibility and to help span the required distance betweenthe termini of the domains, and the two arginines that are present atpositions −1 and 1 of the Oct-1 homeodomain. A glutathione S-transferasedomain (GST) is joined to the amino-terminus of zinc finger 1. FIG. 1Bshows the nucleic acid sequences (SEQ ID NOS.: 1-16) of 16 sitesisolated after four rounds of binding site selection. These sequenceswere used to determine the consensus binding sequence(5′-TAATTANGGGNG3′, SEQ ID NO.: 17) of ZFHD1. FIG. 1C shows thealternative possibilities for homeodomain binding configurationssuggested by the consensus sequence; Mode 1 was determined to be thecorrect optimal configuration for ZFHD1. The letter “N” at a positionindicates that any nucleotide can occupy that position.

FIG. 2A-C is an autoradiograph illustrating the DNA-binding specificityof ZFHD1, the Oct-1 POU domain and the three zinc fingers from Zif268.The probes used are listed at the top of each set of lanes, and theposition of the protein-DNA complex is indicated by the arrow.

FIG. 3 is a graphic representation of the regulation of promoteractivity in vivo by ZFHD1. The expression vector encoded the ZFHD1protein fused to the carboxyl-terminal 81 amino acids of VP16 (+bars),and the empty expression vector Rc/CMV was used as control (-bars). Bargraphs represent the average of three independent trials. Actual valuesand standard deviation reading from left to right are: 1.00±0.05,3.30±0.63; 0.96±0.08, 42.2±5.1; 0.76±0.07, 2.36±0.34; 1.22±0.10,4.22±1.41. Fold induction refers to the level of normalized activityobtained with the ZFHD1-VP16 expression construct divided by thatobtained with Rc/CMV.

FIG. 4. Panel A illustrates data demonstrating that fusion proteinscontaining ZFHD1 linked to either a VP16 or p65 transcription activationdomain activate transcription of a gene encoding secreted alkalinephosphatase (SEAP) linked to ZFHD1 binding sites in HT1080 cells. PanelB illustrates data demonstrating that fusion proteins containing threecopies of the FKBP domain joined to the VP16 or p65 activation domainssupport FK1012-dependent transcription of a reporter gene (secretedalkaline phosphatase) linked to a binding site for the ZFHD1 compositeDNA-binding domain present in the ZFHD1-FKBP(x3) fusion protein. Panel Cillustrates data from an analogous experiment using a wholly syntheticdimerizer in place of FK1012.

FIG. 5 illustrates in schematic form a chimeric transcription factor ofthis invention containing a composite DNA binding domain and atranscription activation domain, bound to its recognized DNA sequence.Also illustrated is a chimeric protein of this invention containing oneor more FKBP domains, a cognate chimeric protein containing a FRAP FRBdomain linked to a transcription activation domain, and a complex ofthose two chimeras formed in the presence of the dimerizer, rapamycin,resulting in the clustering of the transcriptional complex on arecognized DNA sequence.

FIG. 6 illustrates data demonstrating functional dimerizer-dependentexpression of an hGH target gene resulting from complexation of theZFHD1-FKBP(x3) fusion protein to a FRAP FRB-p65 fusion protein andbinding of the complex to a ZFHD1 binding site in engineered cells inwhole animals. These data demonstrate that in vivo administration of adimerizing agent can regulate gene expression in whole animals ofsecreted gene products from cells containing the fusion proteins and aresponsive target gene cassette. Human cells (2×10⁶) transfected withplasmids encoding transcription factors ZFHD1-FKBPx3 and FRB-p65 and atarget gene directing the expression of human growth hormone (hGH) wereinjected into the skeletal muscles of nu/nu mice. Mice were treated withthe indicated concentration of rapamycin by tail vein injection. After17 hours, serum hGH levels were determined by ELISA. Each pointrepresents X±SEM (n=at least 5 per point). Control animals receivedeither engineered cells without drug or drug (10³ or 10⁴ μg/kg) withoutengineered cells.

DETAILED DESCRIPTION OF THE INVENTION

This invention pertains to the design, production and use of chimericproteins containing a composite DNA-binding region, e.g., to obtainconstitutive or regulated expression, repression, cleavage or marking ofa target gene linked to a nucleotide sequence recognized (i.e.,specifically bound) by the chimeric DNA-binding protein. The compositeDNA-binding region is a continuous polypeptide chain spanning at leasttwo heterologous polypeptide portions representing component DNA-bindingdomains. The component polypeptide domains comprise polypeptidesequences derived from at least two different proteins, polypeptidesequences from at least two non-adjacent portions of the same protein,or polypeptide sequences which are not found so linked in nature.

The component polypeptide domains may comprise naturally-occurring ornon-naturally occurring peptide sequence. The chimeric protein mayinclude more than two DNA-binding domains. It may also include one ormore linker regions comprising one or more amino acid residues, orinclude no linker, as appropriate, to join the selected domains. Thenucleic acid sequence recognized by the chimeric DNA-binding protein mayinclude all or a portion of the sequences bound by the componentpolypeptide domains. However, the chimeric protein displays a bindingspecificity that is distinct from the binding specificity of itsindividual polypeptide components.

The invention further involves DNA sequences encoding such chimericproteins, the recombinant DNA sequences to which the chimeric proteinsbind (i.e., which are recognized by the composite DNA-binding region),constructs containing a target gene and a DNA sequence which isrecognized by the chimeric DNA-binding protein, and the use of thesematerials in applications which depend upon specific recognition of anucleotide sequence. Such composite proteins and DNA sequences whichencode them are recombinant in the sense that they contain at least twoconstituent portions which are not otherwise found directly linked(covalently) together in nature, at least not in the order, orientationor arrangement present in the recombinant material. Desirable propertiesof these proteins include high affinity for specific nucleotidesequences, low affinity for most other sequences in a complex genome(such as a mammalian geneome), low dissociation rates from specific DNAsites, and novel DNA recognition specificities distinct from those ofknown natural DNA-binding proteins. A basic principle of the design isthe assembly of multiple DNA-binding domains into a single proteinmolecule that recognizes a long (spanning at least 10 bases, preferablyat least 11 or more bases) and complex DNA sequence with high affinitypresumably through the combined interactions of the individual domains.A further benefit of this design is the potential avidity derived frommultiple independent protein-DNA interactions.

The practice of this invention generally involves expression of a DNAconstruct encoding and capable of directing the expression in a cell ofthe chimeric protein containing the composite DNA-binding region and oneor more optional, additional domains, as described below. Someembodiments also make use of a DNA construct containing a target geneand one or more copies of a DNA sequence to which the chimericDNA-binding protein is capable of binding, preferably with high affinityand/or specificity. Some embodiments further involve one or more DNAconstructs encoding and directing the expression of additional proteinscapable of modulating the activity of the DNA-binding protein, e.g., inthe case of chimeras containing ligand-binding domains which complexwith one another in the presence of a dimerizing ligand.

In one aspect of the invention, the chimeric proteins are transcriptionfactors which may contain one or more regulatory domains in addition tothe composite DNA-binding region. The term “transcription factor” isintended to encompass any protein that regulates gene transcription, andincludes regulators that have a positive or a negative effect ontranscription initiation or progression. Transcription factors mayoptionally contain one or more regulatory domains. The term “regulatorydomain” is defined as any domain which regulates transcription, andincludes both activation domains and repression domains. The term“activation domain” denotes a domain in a transcription factor whichpositively regulates (turns on or increases) the rate of genetranscription. The term “repression domain” denotes a domain in atranscription factor which negatively regulates (turns off, inhibits ordecreases) the rate of gene transcription. The nucleic acid sequencebound by a transcription factor is typically DNA outside the codingregion, such as within a promoter or regulatory element region. However,sufficiently tight binding to nucleotides at other locations, e.g.,within the coding sequence, can also be used to regulate geneexpression.

Preferably the chimeric DNA binding protein binds to a corresponding DNAsequence selectively, i.e., observably binds to that DNA sequencedespite the presence of numerous alternative candidate DNA sequences.Preferably, binding of the chimeric DNA-binding protein to the selectedDNA sequence is at least two, more preferably three and even morepreferably more than four orders of magnitude greater than binding toany one alternative DNA sequence, as may be measured by relative Kdvalues or by relative rates or levels of transcription of genesassociated with the selected and any alternative DNA sequences. It isalso preferred that the selected DNA sequence be recognized to asubstantially greater degree by the chimeric protein containing thecomposite DNA-binding region than by a protein containing only some ofthe individual polypeptide components thereof. Thus, for example, targetgene expression is preferably two, more preferably three, and even morepreferably more than four orders of magnitude greater in the presence ofa chimeric transcription factor containing a composite DNA-bindingregion than in the presence of a protein containing only some of thecomponents of that composite DNA-binding region.

Additional guidance for practicing various aspects of the invention,together with additional illustrations are provided below.

1. Design of Composite DNA-binding Regions. Each composite DNA-bindingregion consists of a continuous polypeptide region containing two ormore component heterologous polypeptide portions which are individuallycapable of recognizing (i.e., binding to) specific nucleotide sequences.The individual component portions may be separated by a linkercomprising one or more amino acid residues intended to permit thesimultaneous contact of each component polypeptide portion with the DNAtarget. The combined action of the composite DNA-binding region formedby the component DNA-binding modules is thought to result in theaddition of the free energy decrement of each set of interactions. Theeffect is to achieve a DNA-protein interaction of very high affinity,preferably with dissociation constant below 10⁻⁹ M, more preferablybelow 10⁻¹⁰ M, even more preferably below 10⁻¹¹ M. This goal is oftenbest achieved by combining component polypeptide regions that bind DNApoorly on their own, that is with low affinity, insufficient forfunctional recognition of DNA under typical conditions in a mammaliancell. Because the hybrid protein exhibits affinity for the compositesite several orders of magnitude higher than the affinities of theindividual sub-domains for their subsites, the protein preferentially(preferably exclusively) occupies the “composite” site which typicallycomprises a nucleotide sequence spanning the individual DNA sequencerecognized by the individual component polypeptide portions of thecomposite DNA-binding region.

Suitable component DNA-binding polypeptides for incorporation into acomposite region have one or more, preferably more, of the followingproperties. They bind DNA as monomers, although dimers can beaccommodated. They should have modest affinities for DNA, withdissociation constants preferably in the range of 10⁻⁶ to 10⁻⁹ M. Theyshould optimally belong to a class of DNA-binding domains whosestructure and interaction with DNA are well understood and thereforeamenable to manipulation. For gene therapy applications, they arepreferably derived from human proteins.

A structure-based strategy of fusing known DNA-binding modules has beenused to design transcription factors with novel DNA-bindingspecificities. In order to visualize how certain DNA-binding domainsmight be fused to other DNA-binding domains, computer modeling studieshave been used to superimpose and align various protein-DNA complexes.

Two criteria suggest which alignments of DNA-binding domains havepotential for combination into a composite DNA-binding region (1) lackof collision between domains, and (2) consistent positioning of thecarboxyl- and amino-terminal regions of the domains, i.e., the domainsmust be oriented such that the carboxyl-terminal region of onepolypeptide can be joined to the amino-terminal region of the nextpolypeptide, either directly or by a linker (indirectly). Domainspositioned such that only the two amino-terminal regions are adjacent toeach other or only the two carboxyl-terminal regions are adjacent toeach other are not suitable for inclusion in the chimeric proteins ofthe present invention. When detailed structural information about theprotein-DNA complexes is not available, it may be necessary toexperiment with various endpoints, and more biochemical work may benecessary to characterize the DNA-binding properties of the chimericproteins. This optimization can be performed using known techniques.Virtually any domains satisfying the above-described criteria arecandidates for inclusion in the chimeric protein. Alternatively,non-computer modeling may also be used.

2. Examples of suitable component DNA-binding domains. DNA-bindingdomains with appropriate DNA binding properties may be selected fromseveral different types of natural DNA-binding proteins. One classcomprises proteins that normally bind DNA only in conjunction withauxiliary DNA-binding proteins, usually in a cooperative fashion, whereboth proteins contact DNA and each protein contacts the other. Examplesof this class include the homeodomain proteins, many of which bind DNAwith low affinity and poor specificity, but act with high levels ofspecificity in vivo due to interactions with partner DNA-bindingproteins. One well-characterized example is the yeast alpha2 protein,which binds DNA only in cooperation with another yeast protein Mcm1.Another example is the human homeodomain protein Phox1, which interactscooperatively with the human transcription factor, serum response factor(SRF).

The homeodomain is a highly conserved DNA-binding domain which has beenfound in hundreds of transcription factors (Scott et al., Biochim.Biophys. Acta 989:25-48 (1989) and Rosenfeld, Genes Dev. 5:897-907(1991)). The regulatory function of a homeodomain protein derives fromthe specificity of its interactions with DNA and presumably withcomponents of the basic transcriptional machinery, such as RNApolymerase or accessory transcription factors (Laughon, Biochemistry30(48):11357 (1991)). A typical homeodomain comprises an approximately61-amino acid residue polypeptide chain, folded into three alhphahelices which binds to DNA.

A second class comprises proteins in which the DNA-binding domain iscomprised of multiple reiterated modules that cooperate to achievehigh-affinity binding of DNA. An example is the C2H2 class ofzinc-finger proteins, which typically contain a tandem array of from twoor three to dozens of zinc-finger modules. Each module contains analpha-helix capable of contacting a three base-pair stretch of DNA.Typically, at least three zinc-fingers are required for high-affinityDNA binding. Therefore, one or two zinc-fingers constitute alow-affinity DNA-binding domain with suitable properties for use as acomponent in this invention. Examples of proteins of the C2H2 classinclude TFIIIA, Zif268, Gli, and SRE-ZBP. (These and other proteins andDNA sequences referred to herein are well known in the art. Theirsources and sequences are known.)

The zinc finger motif, of the type first discovered in transcriptionfactor IIIA (Miller et al., EMBO J. 4:1609 (1985)), offers an attractiveframework for studies of transcription factors with novel DNA-bindingspecificities. The zinc finger is one of the most common eukaryoticDNA-binding motifs (Jacobs, EMBO J. 11:4507 (1992)), and this family ofproteins can recognize a diverse set of DNA sequences (Pavletich andPabo, Science 261:1701 (1993)). Crystallographic studies of theZif268-DNA complex and other zinc finger-DNA complexes show thatresidues at four positions within each finger make most of the basecontacts, and there has been some discussion about rules that mayexplain zinc finger-DNA recognition (Desjarlais and Berg, PNAS 89:7345(1992) and Klevit, Science 253:1367 (1991)). However, studies have alsoshown that zinc fingers can dock against DNA in a variety of ways(Pavletich and Pabo (1993) and Fairall et al., Nature 366:483 (1993)).

A third general class comprises proteins that themselves containmultiple independent DNA-binding domains. Often, any one of thesedomains is insufficient to mediate high-affinity DNA recognition, andcooperation with a covalently linked partner domain is required.Examples include the POU class, such as Oct-1, Oct-2 and Pit-1, whichcontain both a homeodomain and a POU-specific domain; HNF1, which isorganized similarly to the POU proteins; certain Pax proteins (examples:Pax-3, Pax-6), which contain both a homeodomain and a paired box/domain;and XXX, which contains a homeodomain and multiple zinc-fingers of theC2H2 class.

From a structural perspective, DNA-binding proteins containing domainssuitable for use as polypeptide components of a composite DNA-bindingregion may be classified as DNA-binding proteins with a helix-turn-helixstructural design, including, but not limited to, MAT α1, MAT α2, MATa1, Antennapedia, Ultrabithorax, Engrailed, Paired, Fushi tarazu, HOX,Unc86, and the previously noted Oct1, Oct2 and Pit; zinc fingerproteins, such as Zif268, SWI5, Krüppel and Hunchback; steroidreceptors; DNA-binding proteins with the helix-loop-helix structuraldesign, such as Daughterless, Achaete-scute (T3), MyoD, E12 and E47; andother helical motifs like the leucine-zipper, which includes GCN4,C/EBP, c-Fos/c-Jun and JunB. The amino acid sequences of the componentDNA-binding domains may be naturally-occurring ornon-naturally-occurring (or modified).

The choice of component DNA-binding domains may be influenced by anumber of considerations, including the species, system and cell typewhich is targeted; the feasibility of incorporation into a chimericprotein, as may be shown by modeling; and the desired application orutility. The choice of DNA-binding domains may also be influenced by theindividual DNA sequence specificity of the domain and the ability of thedomain to interact with other proteins or to be influenced by aparticular cellular regulatory pathway. Preferably, the distance betweendomain termini is relatively short to facilitate use of the shortestpossible linker or no linker. The DNA-binding domains can be isolatedfrom a naturally-occurring protein, or may be a synthetic molecule basedin whole or in part on a naturally-occurring domain.

An additional strategy for obtaining component DNA-binding domains withproperties suitable for this invention is to modify an existingDNA-binding domain to reduce its affinity for DNA into the appropriaterange. For example, a homeodomain such as that derived from the humantranscription factor Phox1, may be modified by substitution of theglutamine residue at position 50 of the homeodomain. Substitutions atthis position remove or change an important point of contact between theprotein and one or two base pairs of the 6-bp DNA sequence recognized bythe protein. Thus, such substitutions reduce the free energy of bindingand the affinity of the interaction with this sequence and may or maynot simultaneously increase the affinity for other sequences. Such areduction in affinity is sufficient to effectively eliminate occupancyof the natural target site by this protein when produced at typicallevels in mammalian cells. But it would allow this domain to contributebinding energy to and therefore cooperate with a second linkedDNA-binding domain. Other domains that amenable to this type ofmanipulation include the paired box, the zinc-finger class representedby steroid hormone receptors, the myb domain, and the ets domain.

3. Design of linker sequence for covalently linked composite DBDs. Thecontinuous polypeptide span of the composite DNA-binding domain maycontain the component polypeptide modules linked directly end-to-end orlinked indirectly via an intervening amino acid or peptide linker. Alinker moiety may be designed or selected empirically to permit theindependent interaction of each component DNA-binding domain with DNAwithout steric interference. A linker may also be selected or designedso as to impose specific spacing and orientation on the DNA-bindingdomains. The linker amino acids may be derived from endogenous flankingpeptide sequence of the component domains or may comprise one or moreheterologous amino acids. Linkers may be designed by modeling oridentified by experimental trial.

The linker may be any amino acid sequence that results in linkage of thecomponent domains such that they retain the ability to bind theirrespective nucleotide sequences. In some embodiments it is preferablethat the design involve an arrangement of domains which requires thelinker to span a relatively short distance, preferably less than about10 Å. However, in certain embodiments, depending upon the selectedDNA-binding domains and the configuration, the linker may span adistance of up to about 50 Å. For instance, the ZFHD1 protein contains aglycine-glycine-arginine-arginine linker which joins thecarboxyl-terminal region of zinc finger 2 to the amino-terminal regionof the Oct-1 homeodomain.

Within the linker, the amino acid sequence may be varied based on thepreferred characteristics of the linker as determined empirically or asrevealed by modeling. For instance, in addition to a desired length,modeling studies may show that side groups of certain nucleotides oramino acids may interfere with binding of the protein. The primarycriterion is that the linker join the DNA-binding domains in such amanner that they retain their ability to bind their respective DNAsequences, and thus a linker which interferes with this ability isundesirable. A desirable linker should also be able to constrain therelative three-dimensional positioning of the domains so that onlycertain composite sites are recognized by the chimeric protein. Otherconsiderations in choosing the linker include flexibility of the linker,charge of the linker and selected binding domains, and presence of someamino acids of the linker in the naturally-occurring domains. The linkercan also be designed such that residues in the linker contact DNA,thereby influencing binding affinity or specificity, or to interact withother proteins. For example, a linker may contain an amino acid sequencewhich can be recognized by a protease so that the activity of thechimeric protein could be regulated by cleavage. In some cases,particularly when it is necessary to span a longer distance between thetwo DNA-binding domains or when the domains must be held in a particularconfiguration, the linker may optionally contain an additional foldeddomain.

4. Additional domains. Additional domains may be included in the variouschimeric proteins of this invention, e.g. A nuclear localizationsequence, a transcription regulatory domain, a ligand binding domain, aprotein-binding domain, a domain capable of cleaving a nucleic acid,etc.

For example, in some embodiments the chimeric proteins will contain acellular targeting sequence which provides for the protein to betranslocated to the nucleus. Typically a nuclear localization sequencehas a plurality of basic amino acids, referred to as a bipartite basicrepeat (reviewed in Garcia-Bustos et al, Biochimica et Biophysica Acta(1991) 1071, 83-101). This sequence can appear in any portion of themolecule internal or proximal to the N- or C-terminus and results in thechimeric protein being localized inside the nucleus.

The chimeric proteins may include domains that facilitate theirpurification, e.g. “histidine tags” or a glutathione-Stransferasedomain. They may include “epitope tags” encoding peptides recognized byknown monoclonal antibodies for the detection of proteins within cellsor the capture of proteins by antibodies in vitro.

A chimeric DNA-binding protein which contains a domain with endonucleaseactivity (a cleavage domain) can also be used as a novelsequence-specific restriction endonucleases to cleave DNA adjacent tothe recognition sequence bound by the chimeric protein. For example,such a chimeric protein may containing a composite DNA-binding regio andthe C-terminal cleavage domain of Fok I endonuclease, which hasnonspecific DNA-cleavage activity (Li et al., Proc. Natl. Acad. Sci. USA89:4275-4279 (1992)).

Site-specific restriction enzymes can also be linked to otherDNA-binding domains to generate endonucleases with very strict sequencerequirements. The chimeric DNA-binding proteins can also be fused toother domains that can control the stability, association andsubcellular localization of the new proteins.

The chimeric protein may also include one or more transcriptionalactivation domains, such as the well-characterized domain from the viralprotein VP16 or novel activation domains of different designs. Forinstance, one may use one or multiple copies of transcriptionalactivating motifs from human proteins, including e.g. the 18 amino acid(NFLQLPQQTQGALLTSQP, SEQ ID NO: 31) glutamine rich region of Oct-2, theN-terminal 72 amino acids of p53, the SYGQQS repeat in Ewing sarcomagene or an 11 amino acid (535-545) acidic rich region of Rel A protein.Chimeric proteins which contain both a composite DNA-binding domain anda transcriptional activating domain thus comprise compositetranscription factors capable of actuating transcription of a targetgene linked to a DNA sequence recognized by the chimeric protein. Thechimeric proteins may include regulatory domains that place the functionof the DNA-binding domain under the control of an external ligand; oneexample would be the ligand-binding domain of steroid receptors.

The chimeric proteins may also include a ligand-binding domain toprovide for regulatable interaction of the protein with a secondpolypeptide chain. In such cases, the presence of a ligand-bindingdomain permits association of the chimeric DNA-binding protein, in thepresence of a dimerizing ligand, with a second chimeric proteincontaining a transcriptional regulatory domain (activator or repressor)and another ligand-binding domain. Upon dimerization of the chimeras acomposite DNA-binding protein complex is formed which further containsthe transcriptional regulatory domain and any other optional domains.

Multimerizing ligands useful in practicing this invention aremultivalent, i.e., capable of binding to, and thus multimerizing, two ormore of the chimeric protein molecules. The multimerizing ligand maybind to the chimeras containing such ligand-binding domains, in eitherorder or simultaneously, preferably with a Kd value below about 10⁻⁶,more preferably below about 10⁻⁷, even more preferably below about 10⁻⁸,and in some embodiments below about 10⁻⁹ M. The ligand preferably is nota protein or polypeptide and has a molecular weight of less than about 5kDa, preferably below 2 kDa. The ligand-binding domains of the chimericproteins so multimerized may be the same or different. Ligand bindingdomains include among others, various immunophilin domains. One exampleis the FKBP domain which is capable of binding to dimerizing ligandsincorporating FK506 moieties or other FKBP-binding moieties. See e.g.PCT/US93/01617, the full contents of which are hereby incorporated byreference.

Illustrating the class of chimeric proteins of this invention whichcontain a composite DNA-binding domain comprising at least onehomeodomain and at least one zinc finger domain are a set of chimericproteins in which the composite DNA-binding region comprises an Oct-1homeodomain and zinc fingers 1 and 2 of Zif268, referred to herein as“ZFHD1”. Proteins comprising the ZFHD1 composite DNA-binding region havebeen produced and shown to bind a composite DNA sequence (SEQ ID NO.:17) which includes the nucleic acid sequences bound by the relevantportion of the two component DNA-binding proteins.

Illustrating the class of chimeric DNA-binding proteins of thisinvention which further contain at least one transcription activationdomain are chimeric proteins containing the ZFHD1 composite DNA-bindingregion and the Herpes Simplex Virus VP16 activation domain, which hasbeen produced and shown to activate transcription selectively in vivo ofa gene (the luciferase gene) linked to an iterated ZFHD1 binding site.Another chimeric protein containing ZFHD1 and a NF-κB p65 activationdomain has also been produced and shown to activate transcription invivo of a gene (secreted alkaline phosphatase) linked to iterated ZFHD1binding sites.

Transcription factors can be tested for activity in vivo using a simpleassay (F. M. Ausubel et al., Eds., CURRENT PROTOCOLS IN MOLECULARBIOLOGY (John Wiley & Sons, New York, 1994); de Wet et al., Mol. CellBiol. 7:725 (1987)). The in vivo assay requires a plasmid containing andcapable of directing the expression of a recombinant DNA sequenceencoding the transcription factor. The assay also requires a plasmidcontaining a reporter gene, e.g., the luciferase gene, thechloramphenicol acetyl transferase (CAT) gene, secreted alkalinephosphatase or the human growth hormone (hGH) gene, linked to a bindingsite for the transcription factor. The two plasmids are introduced intohost cells which normally do not produce interfering levels of thereporter gene product. A second group of cells, which also lack both thegene encoding the transcription factor and the reporter gene, serves asthe control group and receives a plasmid containing the gene encodingthe transcription factor and a plasmid containing the test gene withoutthe binding site for the transcription factor.

The production of mRNA or protein encoded by the reporter gene ismeasured. An increase in reporter gene expression not seen in thecontrols indicates that the transcription factor is a positive regulatorof transcription. If reporter gene expression is less than that of thecontrol, the transcription factor is a negative regulator oftranscription.

Optionally, the assay may include a transfection efficiency controlplasmid. This plasmid expresses a gene product independent of the testgene, and the amount of this gene product indicates roughly how manycells are taking up the plasmids and how efficiently the DNA is beingintroduced into the cells. Additional guidance on evaluating chimericproteins of this invention is provided below.

5. Design and assembly of constructs. DNA sequences encoding individualDNA-binding sub-domains and linkers, if any, are joined such that theyconstitute a single open reading frame encoding a chimeric proteincontaining the composite DNA-binding region and capable of beingtranslated in cells or cell lysates into a single polypeptide harboringall component domains. This protein-encoding DNA sequence is then placedinto a conventional plasmid vector that directs the expression of theprotein in the appropriate cell type. For testing of proteins anddetermination of binding specificity and affinity, it may be desirableto construct plasmids that direct the expression of the protein inbacteria or in reticulocyte-lysate systems. For use in the production ofproteins in mammalian cells, the protein-encoding sequence is introducedinto an expression vector that directs expression in these cells.Expression vectors suitable for such uses are well known in the art.Various sorts of such vectors are commercially available.

In embodiments involving composite DNA-binding proteins or accessorychimeric proteins which contain multiple domains, e.g. proteinscontaining a ligand binding domain and/or a transcription regulatorydomain, DNA sequences encoding the constituent domains, with anyintroduced sequence alterations may be ligated or otherwise joinedtogether such that they constitute a single open reading frame that canbe translated in cells into a single polypeptide harboring allconstituent domains. The order and arrangement of the domains within thepolypeptide can vary as desired.

6. Target DNA sequence. The DNA sequences recognized by a chimericprotein containing a composite DNA-binding domain can be determinedexperimentally, as described below, or the proteins can be manipulatedto direct their specificity toward a desired sequence. A desirablenucleic acid recognition sequence consists of a nucleotide sequencespanning at least ten, preferably eleven, and more preferably twelve ormore bases. The component binding portions (putative or demonstrated)within the nucleotide sequence need not be fully contiguous; they may beinterspersed with “spacer” base pairs that need not be directlycontacted by the chimeric protein but rather impose proper spacingbetween the nucleic acid subsites recognized by each module. Thesesequences should not impart expression to linked genes when introducedinto cells in the absence of the engineered DNA-binding protein.

To identify a nucleotide sequence that is recognized by a chimericprotein containing the composite DNA-binding region, preferablyrecognized with high affinity (dissociation constant 10⁻¹¹ M or lowerare especially preferred), several methods can be used. If high-affinitybinding sites for individual subdomains of the composite DNA-bindingregion are already known, then these sequences can be joined withvarious spacing and orientation and the optimum configuration determinedexperimentally (see below for methods for determining affinities).Alternatively, high-affinity binding sites for the protein or proteincomplex can be selected from a large pool of random DNA sequences byadaptation of published methods (Pollock, R. and Treisman, R., 1990, Asensitive method for the determination of protein-DNA bindingspecificities. Nucl. Acids Res. 18, 6197-6204). Bound sequences arecloned into a plasmid and their precise sequence and affinity for theproteins are determined. From this collection of sequences, individualsequences with desirable characteristics (i.e., maximal affinity forcomposite protein, minimal affinity for individual subdomains) areselected for use. Alternatively, the collection of sequences is used toderive a consensus sequence that carries the favored base pairs at eachposition. Such a consensus sequence is synthesized and tested (seebelow) to confirm that it has an appropriate level of affinity andspecificity.

7. Design of target gene construct. A DNA construct that enables thetarget gene to be regulated, cleaved, etc. by DNA-binding proteins ofthis invention is a fragment, plasmid, or other nucleic acid vectorcarrying a synthetic transcription unit typically consisting of: (1) onecopy or multiple copies of a DNA sequence recognized with high-affinityby the composite DNA-binding protein; (2) a promoter sequence consistingminimally of a TATA box and initiator sequence but optionally includingother transcription factor binding sites; (3) sequence encoding thedesired product (protein or RNA), including sequences that promote theinitiation and termination of translation, if appropriate; (4) anoptional sequence consisting of a splice donor, splice acceptor, andintervening intron DNA; and (5) a sequence directing cleavage andpolyadenylation of the resulting RNA transcript.

8. Determination of binding affinity. A number of well-characterizedassays are available for determining the binding affinity, usuallyexpressed as dissociation constant, for DNA-binding proteins and thecognate DNA sequences to which they bind. These assays usually requirethe preparation of purified protein and binding site (usually asynthetic oligonucleotide) of known concentration and specific activity.Examples include electrophoretic mobility-shift assays, DNaseIprotection or “footprinting”, and filter-binding. These assays can alsobe used to get rough estimates of association and dissociation rateconstants. These values may be determined with greater precision using aBIAcore instrument. In this assay, the synthetic oligonucleotide isbound to the assay “chip,” and purified DNA-binding protein is passedthrough the flow-cell. Binding of the protein to the DNA immobilized onthe chip is measured as an increase in refractive index. Once protein isbound at equilibrium, buffer without protein is passed over the chip,and the dissociation of the protein results in a return of therefractive index to baseline value. The rates of association anddissociation are calculated from these curves, and the affinity ordissociation constant is calculated from these rates. Binding rates andaffinities for the high affinity composite site may be compared with thevalues obtained for subsites recognized by each subdomain of theprotein. As noted above, the difference in these dissociation constantsshould be at least two orders of magnitude and preferably three orgreater.

9. Testing for function in vivo. Several tests of increasing stringencymay be used to confirm the satisfactory performance of a DNA-bindingprotein designed according to this invention. All share essentially thesame components: (1) (a) an expression plasmid directing the productionof a chimeric protein comprising the composite DNA-binding region and apotent transcriptional activation domain or (b) one or more expressionplasmids directing the production of a pair of chimeric proteins of thisinvention which are capable of dimerizing in the presence of acorresponding dimerizing agent, and thus forming a protein complexcontaining a composite DNA-binding region on one protein and atranscription activation domain on the other; and (2) a reporter plasmiddirecting the expression of a reporter gene, preferably identical indesign to the target gene described above (i.e., multiple binding sitesfor the DNA-binding domain, a minimal promoter element, and a gene body)but encoding any conveniently measured protein.

In a transient transfection assay, the above-mentioned plasmids areintroduced together into tissue culture cells by any conventionaltransfection procedure, including for example calcium phosphatecoprecipitation, electroporation, and lipofection. After an appropriatetime period, usually 24-48 hr, the cells are harvested and assayed forproduction of the reporter protein. In embodiments requiringdimerization of chimeric proteins for activation of transcription, theassay is conducted in the presence of the dimerizing agent. In anappropriately designed system, the reporter gene should exhibit littleactivity above background in the absence of any co-transfected plasmidfor the composite transcription factor (or in the absence of dimerizingagent in embodiments under dimerizer control). In contrast, reportergene expression should be elevated in a dose-dependent fashion by theinclusion of the plasmid encoding the composite transcription factor (orplasmids encoding the multimerizable chimeras, following addition ofmultimerizing agent). This result indicates that there are few naturaltranscription factors in the recipient cell with the potential torecognize the tested binding site and activate transcription and thatthe engineered DNA-binding domain is capable of binding to this siteinside living cells.

The transient transfection assay is not an extremely stringent test inmost cases, because the high concentrations of plasmid DNA in thetransfected cells lead to unusually high concentrations of theDNA-binding protein and its recognition site, allowing functionalrecognition even with relative low affinity interactions. A morestringent test of the system is a transfection that results in theintegration of the introduced DNAs at near single-copy. Thus, both theprotein concentration and the ratio of specific to non-specific DNAsites would be very low; only very high affinity interactions would beexpected to be productive. This scenario is most readily achieved bystable transfection in which the plasmids are transfected together withanother DNA encoding an unrelated selectable marker (e.g.,G418-resistance). Transfected cell clones selected for drug resistancetypically contain copy numbers of the nonselected plasmids ranging fromzero to a few dozen. A set of clones covering that range of copy numberscan be used to obtain a reasonably clear estimate of the efficiency ofthe system.

Perhaps the most stringent test involves the use of a viral vector,typically a retrovirus, that incorporates both the reporter gene and thegene encoding the composite transcription factor or multimerizablecomponents thereof. Virus stocks derived from such a construction willgenerally lead to single-copy transduction of the genes.

If the ultimate application is gene therapy, it may be preferred toconstruct transgenic animals carrying similar DNAs to determine whetherthe protein is functional in an animal.

11. Introduction of Constructs into Cells

Constructs encoding the chimeras containing a composite DNA-bindingregion, constructs encoding related chimeric proteins (e.g. in the caseof ligand-dependent applications) and constructs directing theexpression of target genes, all as described herein, can be introducedinto cells as one or more DNA molecules or constructs, in many cases inassociation with one or more markers to allow for selection of hostcells which contain the construct(s). The constructs can be prepared inconventional ways, where the coding sequences and regulatory regions maybe isolated, as appropriate, ligated, cloned in an appropriate cloninghost, analyzed by restriction or sequencing, or other convenient means.Particularly, using PCR, individual fragments including all or portionsof a functional unit may be isolated, where one or more mutations may beintroduced using “primer repair”, ligation, in vitro mutagenesis, etc.as appropriate. The construct(s) once completed and demonstrated to havethe appropriate sequences may then be introduced into a host cell by anyconvenient means. The constructs may be integrated and packaged intonon-replicating, defective viral genomes like Adenovirus,Adeno-associated virus (AAV), or Herpes simplex virus (HSV) or others,including retroviral vectors, for infection or transduction into cells.The constructs may include viral sequences for transfection, if desired.Alternatively, the construct may be introduced by fusion,electroporation, biolistics, transfection, lipofection, or the like. Thehost cells will in some cases be grown and expanded in culture beforeintroduction of the construct(s), followed by the appropriate treatmentfor introduction of the construct(s) and integration of theconstruct(s). The cells will then be expanded and screened by virtue ofa marker present in the construct. Various markers which may be usedsuccessfully include hprt, neomycin resistance, thymidine kinase,hygromycin resistance, etc.

In some instances, one may have a target site for homologousrecombination, where it is desired that a construct be integrated at aparticular locus. For example, one can delete and/or replace anendogenous gene (at the same locus or elsewhere) with a recombinanttarget construct of this invention. For homologous recombination, onemay generally use either Ω or O-vectors. See, for example, Thomas andCapecchi, Cell (1987) 51, 503-512; Mansour, et al., Nature (1988) 336,348-352; and Joyner, et al., Nature (1989) 338, 153-156.

The constructs may be introduced as a single DNA molecule encoding allof the genes, or different DNA molecules having one or more genes. Theconstructs may be introduced simultaneously or consecutively, each withthe same or different markers.

Vectors containing useful elements such as bacterial or yeast origins ofreplication, selectable and/or amplifiable markers, promoter/enhancerelements for expression in procaryotes or eucaryotes, etc. which may beused to prepare stocks of construct DNAs and for carrying outtransfections are well known in the art, and many are commerciallyavailable.

12. Introduction of Constructs into Animals

Cells which have been modified ex vivo with the DNA constructs may begrown in culture under selective conditions and cells which are selectedas having the desired construct(s) may then be expanded and furtheranalyzed, using, for example, the polymerase chain reaction fordetermining the presence of the construct in the host cells. Oncemodified host cells have been identified, they may then be used asplanned, e.g. grown in culture or introduced into a host organism.

Depending upon the nature of the cells, the cells may be introduced intoa host organism, e.g. a mammal, in a wide variety of ways. Hematopoieticcells may be administered by injection into the vascular system, therebeing usually at least about 10⁴ cells and generally not more than about10¹⁰, more usually not more than about 10⁸ cells. The number of cellswhich are employed will depend upon a number of circumstances, thepurpose for the introduction, the lifetime of the cells, the protocol tobe used, for example, the number of administrations, the ability of thecells to multiply, the stability of the therapeutic agent, thephysiologic need for the therapeutic agent, and the like. Alternatively,with skin cells which may be used as a graft, the number of cells woulddepend upon the size of the layer to be applied to the burn or otherlesion. Generally, for myoblasts or fibroblasts, the number of cellswill be at least about 10⁴ and not more than about 108 and may beapplied as a dispersion, generally being injected at or near the site ofinterest. The cells will usually be in a physiologically-acceptablemedium.

Cells engineered in accordance with this invention may also beencapsulated, e.g. using conventional materials and methods. See e.g.Uludag and Sefton, 1993, J Biomed. Mater. Res. 27(10):1213-24; Chang etal, 1993, Hum Gene Ther 4(4):433-40; Reddy et al, 1993, J Infect Dis168(4):1082-3; Tai and Sun, 1993, FASEB J 7(11):1061-9; Emerich et al,1993, Exp Neurol 122(1):37-47; Sagen et al, 1993, J Neurosci13(6):2415-23; Aebischer et al, 1994, Exp Neurol 126(2):151-8; Savelkoulet al, 1994, J Immunol Methods 170(2):185-96; Winn et al, 1994, PNAS USA91(6):2324-8; Emerich et al, 1994, Prog Neuropsychopharmacol BiolPsychiatry 18(5):935-46 and Kordower et al, 1994, PNAS USA91(23):10898-902. The cells may then be introduced in encapsulated forminto an animal host, preferably a mammal and more preferably a humansubject in need thereof. Preferably the encapsulating material issemipermeable, permitting release into the host of secreted proteinsproduced by the encapsulated cells. In many embodiments thesemipermeable encapsulation renders the encapsulated cellsimmunologically isolated from the host organism in which theencapsulated cells are introduced. In those embodiments the cells to beencapsulated may express one or more chimeric proteins containingcomponents domains derived from viral proteins or proteins from otherspecies.

Instead of ex vivo modification of the cells, in many situations one maywish to modify cells in vivo. For this purpose, various techniques havebeen developed for modification of target tissue and cells in vivo. Anumber of virus vectors have been developed, such as adenovirus,adeno-associated virus. and retroviruses, which allow for transfectionand random integration of the virus into the host. See, for example,Debunks et al. (1984) Proc. Natl. Acad. Sci. USA 81, 7529-7533; Caned etal., (1989) Science 243, 375-378; Hiebert et al. (1989) Proc. Natl.Acad. Sci. USA 86, 3594-3598; Hatzoglu et al. (1990) J. Biol. Chem. 265,17285-17293 and Ferry, et al. (1991) Proc. Natl. Acad. Sci. USA 88,8377-8381. The vector may be administered by injection, e.g.intravascularly or intramuscularly, inhalation, or other parenteralmode.

In accordance with in vivo genetic modification, the manner of themodification will depend on the nature of the tissue, the efficiency ofcellular modification required, the number of opportunities to modifythe particular cells, the accessibility of the tissue to the DNAcomposition to be introduced, and the like. By employing an attenuatedor modified retrovirus carrying a target transcriptional initiationregion, if desired, one can activate the virus using one of the subjecttranscription factor constructs, so that the virus may be produced andtransfect adjacent cells.

The DNA introduction need not result in integration in every case. Insome situations, transient maintenance of the DNA introduced may besufficient. In this way, one could have a short term effect, where cellscould be introduced into the host and then turned on after apredetermined time, for example, after the cells have been able to hometo a particular site.

13. ZFHD1

Illustrating one design approach, Example 1 describes computer modelingstudies which were used to determine the orientation and linkage ofpotentially useful DNA-binding domains (see Example 1). Computermodeling studies allowed manipulation and superimposition of the crystalstructures of Zif268 and Oct-1 protein-DNA complexes. This study yieldedtwo arrangements of the domains which appeared to be suitable for use ina chimeric protein. In one alignment, the carboxyl-terminal region ofzinc finger 2 was 8.8 Å away from the amino-terminal region of thehomeodomain, suggesting that a short polypeptide could connect thesedomains. In this model, the chimeric protein would bind a hybrid DNAsite with the sequence 5′-AAATNNTGGGCG-3′ (SEQ ID NO.: 18). The Oct-1homeodomain would recognize the AAAT subsite, zinc finger 2 wouldrecognize the TGG subsite, and zinc finger 1 would recognize the GCGsubsite. No risk of steric interference between the domains was apparentin this model. This arrangement was used in the work described below andin the Examples.

The second plausible arrangement would also have a short polypeptidelinker spanning the distance from zinc finger 2 to the homeodomain (lessthan 10 Å); however, the subsites are arranged so that the predictedbinding sequence is 5′-CGCCCANNAAAT-3′ (SEQ ID NO.: 19). Thisarrangement was not explicitly used in the work described below,although the flexibility of the linker region may also allow ZFHD1 torecognize this site.

After selecting a suitable arrangement, construction of thecorresponding molecule was carried out. Generally, sequences may beadded to the chimeric protein to facilitate expression, detection,purification or assays of the product by standard methods. A glutathioneS-transferase domain (GST) was attached to ZFHD1 for these purpose (seeExample 2).

The consensus binding sequence of the chimeric protein ZFHD1 wasdetermined by selective binding studies from a random pool ofoligonucleotides. The oligonucleotide sequences bound by the chimericprotein were sequenced and compared to determine the consensus bindingsequence for the chimeric protein (see Example 3 and FIG. 1).

After four rounds of selection, 16 sites were cloned and sequenced (SEQID NOS.: 1-16, FIG. 1B). Comparing these sequences revealed theconsensus binding site 5′-TAATTANGGGNG-3′ (SEQ ID NO.: 17). The 5′ halfof this consensus, TAATTA, resembled a canonical homeodomain bindingsite TAATNN (Laughon, (1991)), and matched the site (TAATNA) that ispreferred by the Oct-1 homeodomain in the absence of the POU-specificdomain (Verrijzer et al., EMBO J. 11:4993 (1992)). The 3′ half of theconsensus, NGGGNG, was consistent with adjacent binding sites forfingers 2 (TGG) and 1 (GCG) of Zif268.

Binding studies were performed in order to determine the ability of thechimeric protein ZFHD1 to distinguish the consensus sequence from thesequences recognized by the component polypeptides of the compositeDNA-binding region. ZFHD1, the Oct-1 POU domain (containing ahomeodomain and a POU-specific domain), and the three zinc fingers ofZif268 were compared for their abilities to distinguish among the Oct-1site 5′-ATGCAAATGA-3′ (SEQ ID NO.: 20), the Zif268 site 5′-GCGTGGGCG-3′and the hybrid binding site 5′-TAATGATGGGCG-3′ (SEQ ID NO.: 21). Thechimeric protein ZFHD1 preferred the optimal hybrid site to the octamersite by a factor of 240 and did not bind to the Zif site. The POU domainof Oct-1 bound to the octamer site with a dissociation constant of1.8×10⁻¹⁰ M under the assay conditions used, preferring this site to thehybrid sequences by factors of 10 and 30, and did not bind to the Zifsite. The three zinc fingers of Zif268 bound to the Zif site with adissociation constant of 3.3×10⁻¹⁰ M, and did not bind to the otherthree sites. These experiments show that ZFHD1 binds tightly andspecifically to the hybrid site and displayed DNA-binding specificitythat was clearly distinct from that of either of the original proteins.

In order to determine whether the novel DNA-binding protein couldfunction in vivo, ZFHD1 was fused to a transcriptional activation domainto generate a transcription factor, and transfection experiments wereperformed (see Example 5). An expression plasmid encoding ZFHD1 fused tothe carboxyl-terminal 81 amino acids of the Herpes Simplex Virus VP16protein (ZFHD1-VP16) was co-transfected into 293 cells with reporterconstructs containing the SV40 promoter and the firefly luciferase gene(FIG. 3). To determine whether the chimeric protein could specificallyregulate gene expression, reporter constructs containing two tandemcopies of either the ZFHD1 site 5′-TAATGATGGGCG-3′ (SEQ ID NO.: 21), theoctamer site 5′-ATGCAAATGA-3′ (SEQ ID NO.: 20) or the Zif site5′-GCGTGGGCG-3′ inserted upstream of the SV40 promoter were tested. Whenthe reporter contained two copies of the ZFHD1 site, the ZFHD1-VP16protein stimulated the activity of the promoter in a dose-dependentmanner. Furthermore, the stimulatory activity was specific for thepromoter containing the ZFHD1 binding sites. At levels of protein whichstimulated this promoter by 44-fold, no stimulation above background wasobserved for promoters containing the octamer or Zif sites. Thus, ZFHD1efficiently and specifically recognized its target site in vivo.

Utilizing the above-described procedures and known DNA-binding domains,other novel chimeric transcription factor proteins can be constructed.These chimeric proteins can be studied as disclosed herein to determinethe consensus binding sequence of the chimeric protein. The bindingspecificity, as well as the in vivo activity, of the chimeric proteincan also be determined using the procedures illustrated herein. Thus,the methods of this invention can be utilized to create various chimericproteins from the domains of DNA-binding proteins.

14. Optimization and Engineering of Composite DNA-Binding Regions

The useful range of composite DNA binding regions is not limited to thespecifities that can be obtained by linking two naturally occurring DNAbinding subdomains. A variety of mutagenesis methods can be used toalter the binding specificity. These include use of the crystal or NMRstructures (3D) of complexes of a DNA-binding domain (DBD) with DNA torationally predict (an) amino acid substitution(s) that will alter thenucleotide sequence specificity of DNA binding, in combination withcomputational modelling approaches. Candidate mutants can then beengineered and expressed and their DNA binding specificity identifiedusing oligonucleotide site selection and DNA sequencing, as describedearlier.

An alternative approach to generating novel sequence specificities is touse databases of known homologs of the DBD to predict amino acidsubstitutions that will alter binding. For example, analysis ofdatabases of zinc finger sequences has been used to alter the bindingspecificity of a zinc finger (Desjarlais and Berg (1993) Proc. Natl.Acad. Sci. USA 90, 2256-2260).

A further and powerful approach is random mutaganesis of amino acidresidues which may contact the DNA, followed by screening or selectionfor the desired novel specificity. Preferably, the libraries aresurveyed using phage display so that mutants can be directly selected.For example, phage display of the three fingers of Zif268 (including thetwo incorporated into ZFHD1) has been described, and random mutagenesisand selection has been used to alter the specificity and affinity of thefingers (Rebar and Pabo (1994) Science 263, 671-673; Jamieson et al,(1994) Biochemistry 33, 5689-5695; Choo and Klug (1994)Proc. Natl. Acad.Sci. USA 91, 11163-11167; Choo and Klug (1994) Proc. Natl. Acad. Sci.USA 91, 11168-11172; Choo et al (1994) Nature 372, 642-645; Wu et al(1995) Proc. Natl. Acad. Sci USA 92, 344-348). These mutants can beincorporated into ZFHD1 to provide new composite DNA binding regionswith novel nucleotide sequence specificities. Other DBDs may besimilarly altered. If structural information is not available, generalmutagenesis strategies can be used to scan the entire domain fordesirable mutations: for example alanine-scanning mutagenesis(Cunningham and Wells (1989) Science 244, 1081-1085), PCRmisincorporation mutagenesis (see eg. Cadwell and Joyce (1992) PCR Meth.Applic. 2, 28-33), and ‘DNA shuffling’ (Stemmer (1994) Nature 370,389-391). These techniques produce libraries of random mutants, or setsof single mutants, that can then be readily searched by screening orselection approaches such as phage display.

In all these approaches, mutagenesis can be carried out directly on thecomposite DNA binding region, or on the individual subdomain of interestin its natural or other protein context. In the latter case, theengineered component domain with new nucleotide sequence specificity maybe subsequently incorporated into the composite DNA binding region inplace of the starting component. The new DNA binding specificity may bewholly or partially different from that of the initial protein: forexample, if the desired binding specificity contains (a) subsite(s) forknown DNA binding subdomains, other subdomains can be mutated torecognize adjacent sequences and then combined with the natural domainto yield a composite DNA binding region with the desired specificity.

Randomization and selection strategies may be used to incorporate otherdesirable properties into the composite DNA binding regions in additionto altered nucleotide recognition specificity, by imposing anappropriate in vitro selective pressure (for review see Clackson andWells (1994) Trends Biotech. 12, 173-184). These include improvedaffinity, improved stability and improved resistance to proteolyticdegradation.

The ability to engineer binding regions with novel DNA bindingspecificities permits composite DNA binding regions to be designed andproduced to interact specifically with any desired nucleotide sequence.Thus a clinically interesting sequence may be chosen and a composite DNAbinding region engineered to recognize it. For example, composite DNAbinding region may be designed to bind chromosomal breakpoints andrepress transcription of an otherwise activated oncogene (see Choo et al(1994) Nature 372, 642-645); to bind viral DNA or RNA genomes and blockor activate expression of key viral genes; or to specifically bind thecommon mutated versions of a mutational hotspot sequence in an oncogeneand repress transcription (such as the mutation of codon 21 of humanras), and analogously to bind mutated tumor supressor genes and activatetheir transcription.

Additionally, in optimizing chimeric proteins of this invention itshould be appreciated that immunogenicity of a polypeptide sequence isthought to require the binding of peptides by MHC proteins and therecognition of the presented peptides as foreign by endogenous T-cellreceptors. It may be preferable, at least in gene therapy applications,to alter a given foreign peptide sequence to minimize the probability ofits being presented in humans. For example, peptide binding to human MHCclass I molecules has strict requirements for certain residues at key‘anchor’ positions in the bound peptide: eg. HLA-A2 requires leucine,methionine or isoleucine at position 2 and leucine or valine at theC-terminus (for review see Stern and Wiley (1994) Structure 2, 145-251).Thus in engineered proteins, this periodicity of these residues could beavoided.

15. Tissue-Specific or Cell-Type Specific Expression

It may be preferred in certain embodiments that the chimeric protein(s)of this invention be expressed in a cell-specific or tissue-specificmanner. Such specificity of expression may be, achieved by operablylinking one or more of the DNA sequences encoding the chimericprotein(s) to a cell-type specific transcriptional regulatory sequence(e.g. promoter/enhancer). Numerous cell-type specific transcriptionalregulatory sequences are known which may be used for this purpose.Others may be obtained from genes which are expressed in a cell-specificmanner.

For example, constructs for expressing the chimeric proteins may containregulatory sequences derived from known genes for specific expression inselected tissues. Representative examples are tabulated below:

tissue gene reference lens γ2-crystallin Breitman, M. L., Clapoff, S.,Rossant, J., Tsui, L. C., Golde, L. M., Maxwell, I. H., Bernstin, A.(1987) Genetic Ablation: targeted expression of a toxin gene causesmicrophthalmia in transgenic mice. Science 238: 1563-1565 αA-crystallinLandel, C. P., Zhao, J., Bok, D., Evans, G. A. (1988) Lens-specificexpression of a recombinant ricin induces developmental defects in theeyes of transgenic mice. Genes Dev. 2: 1168-78 Kaur, S., Key, B., Stock,J., McNeish, J. D., Akeson, R., Potter, S. S. (1989) Targeted ablationof alpha-crystallin-synthesizing cells produces lens-deficient eyes intransgenic mice. Development 105: 613-619 pituitary Growth hormoneBehringer, R. R., Mathews, L. S., Palmiter, R. D., Brinster, R. L.(1988) Dwarf mice somatrophic produced by genetic ablation of growthhormone-expressing cells. Genes Dev. 2: cells 453-461 pancreas Insulin-Ornitz, D. M., Palmiter, R. D., Hammer, R. E., Brinster, R. L., Swift,G. H., Elastase - acinar MacDonald, R. J. (1985) Specific expression ofan elastase-human growth fusion cell specific in pancreatic acinar cellsof transgeneic mice. Nature 131: 600-603 Palmiter, R. D., Behringer, R.R., Quaife, C. J., Maxwell, F., Maxwell, I. H., Brinster, R. L. (1987)Cell lineage ablation in transgeneic mice by cell-specific expression ofa toxin gene. Cell 50: 435-443 T cells lck promoter Chaffin, K. E.,Beals, C. R., Wilkie, T. M., Forbush, K. A., Simon, M. I., Perlmutter,R. M. (1990) EMBO Journal 9: 3821-3829 B cells Immunoglobulin Borelli,E., Heyman, R., Hsi, M., Evans, R. M. (1988) Targeting of an induciblekappa light chain toxic phenotype in animal cells. Proc. Natl. Acad.Sci. USA 85: 7572-7576 Heyman, R. A., Borrelli, E., Lesley, J.,Anderson, D., Richmond, D. D., Baird, S. M., Hyman, R., Evans, R. M.(1989) Thymidine kinase obliteration: creation of transgenic mice withcontrolled immunodeficiencies. Proc. Natl. Acad. Sci. USA 86: 2698-2702Schwann P₀ promoter Messing, A., Behringer, R. R., Hammang, J. P.Palmiter, R D, Brinster, R L, Lemke, G., cells P0 promoter directsespression of reporter and toxin genes to Schwann cells of transgenicmice. Neuron 8: 507-520 1992 Myelin basic Miskimins, R. Knapp, L.,Dewey, M J, Zhang, X. Cell and tissue-specific protein expression of aheterologous gene under control of the myelin basic protein genepromoter in trangenic mice. Brain Res Dev Brain Res 1992 Vol 65: 217-21spermatids protamine Breitman, M. L., Rombola, H., Maxwell, I. H.,Klintworth, G. K., Bernstein, A. (1990) Genetic ablation in transgenicmice with attenuated diphtheria toxin A gene. Mol. Cell. Biol. 10:474-479 lung Lung surfacant Ornitz, D. M., Palmiter, R. D., Hammer, R.E., Brinster, R. L., Swift, G. H., gene MacDonald, R. J. (1985) Specificexpression of an elastase-human growth fusion in pancreatic acinar cellsof transgeneic mice. Nature 131: 600-603 adipocyte P2 Ross, S. R,Braves, R A, Spiegelman, B M Targeted expression of a toxin gene toadipose tissue: transgenic mice resistant to obesity Genes and Dev 7:1318-24 1993 muscle myosin light Lee, K J, Ross, R S, Rockman, H A,Harris, A N, O'Brien, T X, van-Bilsen, M., chain Shubeita, H E, Kandolf,R., Brem, G., Prices et al J. BIol. Chem. 1992 Aug 5, 267: 15875-85Alpha actin Muscat, G E., Perry, S., Prentice, H. Kedes, L. The humanskeletal alpha-actin gene is regulated by a muscle-specific enhancerthat binds three nuclear factors. Gene Expression 2, 111-26, 1992neurons neuro-filament Reeben, M. Halmekyto, M. Alhonen, L. Sinervirta,R. Saarma, M. Janne, J. Tissue- proteins specific expression of ratlight neurofilament promoter-driven reporter gene in transgenic mice.BBRC 1993: 192: 465-70 liver tyrosine amino- transferase, albumin,apolipo- proteinsIdentification of Tissue Specific Promoters

To identify the sequences that control the tissue- or cell-type specificexpression of a gene, one isolates a genomic copy of the selected geneincluding sequences “upstream” from the exons that code for the protein.

These upstream sequences are then usually fused to an easily detectablereporter gene like beta-galactosidase, in order to be able to follow theexpression of the gene under the control of upstream regulatorysequences.

To establish which upstream sequences are necessary and sufficient tocontrol gene expression in a cell-type specific manner, the completeupstream sequences are introduced into the cells of interest todetermine whether the initial clone contains the control sequences.Reporter gene expression is monitored as evidence of expression.

If these sequences contain the necessary sequences for cell-typespecific expression, deletions (shown schematically above) may be madein the 5′ flanking sequences to determine which sequences are minimallyrequired for cell-type specific expression. This can be done by makingtransgenic mice with each construct and monitoring beta gal expression,or by first examining the expression in specific culture cells, withcomparison to expression in non-specific cultured cells.

Several successive rounds of deletion analysis normally pinpoint theminimal sequences required for tissue specific expression. Ultimately,these sequences are then introduced into transgenic mice to confirm thatthe expression is only detectable in the cells of interest.

16. Applications

A. Constitutive gene therapy. Gene therapy often requires controlledhigh-level expression of a therapeutic gene, sometimes in a cell-typespecific pattern. By supplying saturating amounts of an activatingtranscription factor of this invention to the therapeutic gene,considerably higher levels of gene expression can be obtained relativeto natural promoters or enhancers, which are dependent on endogenoustranscription factors. Thus, one application of this invention to genetherapy is the delivery of a two-transcription-unit cassette (which mayreside on one or two plasmid molecules, depending on the deliveryvector) consisting of (1) a transcription unit encoding a chimericprotein composed of a composite DNA-binding region of this invention anda strong transcription activation domain (e.g., derived from the VP16protein, p65 protein, etc) and (2) a transcription unit consisting ofthe therapeutic gene expressed under the control of a minimal promotercarrying one, and preferably several, binding sites for the compositeDNA-binding domain. Cointroduction of the two transcription units into acell results in the production of the hybrid transcription factor whichin turn activates the therapeutic gene to high level. This strategyessentially incorporates an amplification step, because the promoterthat would be used to produce the therapeutic gene product inconventional gene therapy is used instead to produce the activatingtranscription factor. Each transcription factor has the potential todirect the production of multiple copies of the therapeutic protein.

This method may be employed to increase the efficacy of many genetherapy strategies by substantially elevating the expression of thetherapeutic gene, allowing expression to reach therapeutically effectivelevels. Examples of therapeutic genes that would benefit from thisstrategy are genes that encode secreted therapeutic proteins, such ascytokines, growth factors and other protein hormones, antibodies, andsoluble receptors. Other candidate therapeutic genes are disclosed inPCT/US93/01617.

B. Regulated gene therapy. In many instances, the ability to switch atherapeutic gene on and off at will or the ability to titrate expressionwith precision are essential to therapeutic efficacy. This invention isparticularly well suited for achieving regulated expression of a targetgene. Two examples of how regulated expression may be achieved aredescribed. The first involves a recombinant transcription factor whichcomprises a composite DNA-binding domain, a potent transcriptionalactivation domain, and a regulatory domain controllable by a smallorally-available ligand. One example is the ligand-binding domain ofsteroid receptors, in particular the domain derived from the modifiedprogesterone receptor described by Wang et al, 1994, Proc Natl Acad SciUSA 91:8180-8184. In this example, the composite DNA binding domain ofthis invention is used in place of the GAL4 domain in the recombinanttranscription factor and the target gene is linked to a DNA sequencerecognized by the composite DNA binding domain. Such a design permitsthe regulation of a target gene by known anti-progestins such as RU486.The transcription factors described here greatly enhance the efficacy ofthis regulatory domain because of the enhanced affinity of theDNA-binding domain and the absence of background activity that arisesfrom ligand-independent dimerization directed by the GAL4 domain inpublished constructs.

Another example involves a pair of chimeric proteins, a dimerizing agentcapable of dimerizing the chimeras and a target gene construct to beexpressed. The first chimeric protein comprises a composite DNA-bindingregion as described herein and one or more copies of one or morereceptor domains (e.g. FKBP, cyclophilin, FRB region of FRAP, etc.) forwhich a ligand, preferably a high-affinity ligand, is available. Thesecond chimeric protein comprises an activation domain and one or morecopies of one or more receptor domains (which may be the same ordifferent than on the prior chimeric protein). The dimerizing reagent iscapable of binding to the receptor (or “ligand binding”) domains presenton each of the chimeras and thus of dimerizing or oligomerizing thechimeras. DNA molecules encoding and directing the expression of thesechimeric proteins are introduced into the cells to be engineered. Alsointroduced into the cells is a target gene linked to a DNA sequence towhich the composite DNA-binding domain is capable of binding (if notalready present within the cells). Contacting the engineered cells ortheir progeny with the oligomerizing reagent leads to regulated activityof the transcription factor and hence to expression of the target gene.In cases where the target gene and recognition sequence are alreadypresent within the cell, the activation domain may be replaced by atranscription repressing domain for regulated inhibition of expressionof the target gene. The design and use of similar components isdisclosed in PCT/US93/01617. These may be adapted to the presentinvention by the use of a composite DNA-binding domain, and DNA sequenceencoding it, in place of the alternative DNA-binding domains asdisclosed in the referenced patent document.

The dimerizing ligand may be administered to the patient as desired toactivate transcription of the target gene. Depending upon the bindingaffinity of the ligand, the response desired, the manner ofadministration, the half-life, the number of cells present, variousprotocols may be employed. The ligand may be administered parenterallyor orally. The number of administrations will depend upon the factorsdescribed above. The ligand may be taken orally as a pill, powder, ordispersion; bucally; sublingually; injected intravascularly,intraperitoneally, subcutaneously; by inhalation, or the like. Theligand (and monomeric antagonist compound) may be formulated usingconventional methods and materials well known in the art for the variousroutes of administration. The precise dose and particular method ofadministration will depend upon the above factors and be determined bythe attending physician or human or animal healthcare provider. For themost part, the manner of administration will be determined empirically.

In the event that transcriptional activation by the ligand is to bereversed or terminated, a monomeric compound which can compete with thedimerizing ligand may be administered. Thus, in the case of an adversereaction or the desire to terminate the therapeutic effect, anantagonist to the dimerizing agent can be administered in any convenientway, particularly intravascularly, if a rapid reversal is desired.Alternatively, one may provide for the presence of an inactivationdomain (or transcriptional silencer) with a DNA binding domain. Inanother approach, cells may be eliminated through apoptosis viasignaling through Fas or TNF receptor as described elsewhere. SeeInternational Patent Applications PCT/US94/01617 and PCI/US94/08008.

The particular dosage of the ligand for any application may bedetermined in accordance with the procedures used for therapeutic dosagemonitoring, where maintenance of a particular level of expression isdesired over an extended period of times, for example, greater thanabout two weeks, or where there is repetitive therapy, with individualor repeated doses of ligand over short periods of time, with extendedintervals, for example, two weeks or more. A dose of the ligand within apredetermined range would be given and monitored for response, so as toobtain a time-expression level relationship, as well as observingtherapeutic response. Depending on the levels observed during the timeperiod and the therapeutic response, one could provide a larger orsmaller dose the next time, following the response. This process wouldbe iteratively repeated until one obtained a dosage within thetherapeutic range. Where the ligand is chronically administered, oncethe maintenance dosage of the ligand is determined, one could then doassays at extended intervals to be assured that the cellular system isproviding the appropriate response and level of the expression product.

It should be appreciated that the system is subject to many variables,such as the cellular response to the ligand, the efficiency ofexpression and, as appropriate, the level of secretion, the activity ofthe expression product, the particular need of the patient, which mayvary with time and circumstances, the rate of loss of the cellularactivity as a result of loss of cells or expression activity ofindividual cells, and the like. Therefore, it is expected that for eachindividual patient, even if there were universal cells which could beadministered to the population at large, each patient would be monitoredfor the proper dosage for the individual.

C. Gene Therapy: Endogenous Genes

This invention is adaptable to a number of approaches for gene therapyinvolving regulation of transcription of a gene which is endogenous tothe engineered cells. These approaches involve the use of a chimericprotein as a transcription factor to actuate or increase thetranscription of an endogenous gene whose gene product is beneficial orto inhibit the transcription of an endogenous gene whose gene product isexcessive, disease-causing or otherwise detrimental.

In one approach, a composite DNA-binding domain is designed or selectedwhich is capable of binding to an endogenous nucleotide sequence linkedto the endogenous gene of interest, e.g., a nucleotide sequence locatedwithin or in the vicinity of the promoter region or elsewhere in the DNAsequence flanking the endogenous gene's coding region. Alternatively, aknown recognition sequence for a composite DNA-binding region may beintroduced in proximity to a selected endogenous gene by homologousrecombination to render the endogenous gene responsive to acorresponding chimeric transcription factor of this invention. See e.g.Gu et al., Science 265, 103-106 (1994). Constructs are made as describedelsewhere which encode a chimeric protein containing the compositeDNA-binding region and a transcription activation domain. Introductioninto cells of the DNA construct permitting expression of the chimerictranscription factor leads to specific activation of transcription ofthe endogenous gene linked to the recognition sequence for the chimericprotein. Repression or inhibition of expression of the target gene maybe effected using a chimeric protein containing the compositeDNA-binding region, which may also contain an optional transcriptioninhibiting domain as described elsewhere. Again, as discussed elsewhere,the DNA construct may be designed to permit regulated expression of thechimeric protein, e.g. by use of an inducible promoter or by use of anyof the regulatable gene therapy approaches which are known in the art.Likewise the construct may be under the control of a tissue specificpromoter or enhancer, permitting tissue-specific or cell-type-specificexpression of the chimera and regulation of the endogenous gene.Finally, it should be noted that constructs encoding a pair oftranscription factors containing ligand-binding domains permittingligand-dependent function may be used in place of a single transcriptionfactor construct.

D. Production of recombinant proteins and viruses. Production ofrecombinant therapeutic proteins for commercial and investigationalpurposes is often achieved through the use of mammalian cell linesengineered to express the protein at high level. The use of mammaliancells, rather than bacteria or yeast, is indicated where the properfunction of the protein requires post-translational modifications notgenerally performed by heterologous cells. Examples of proteins producedcommercially this way include erythropoietin, tissue plasminogenactivator, clotting factors such as Factor VIII:c, antibodies, etc. Thecost of producing proteins in this fashion is directly related to thelevel of expression achieved in the engineered cells. Thus, because theconstitutive two-transcription-unit system described above can achieveconsiderably higher expression levels than conventional expressionsystems, it may greatly reduce the cost of protein production. A secondlimitation on the production of such proteins is toxicity to the hostcell: Protein expression may prevent cells from growing to high density,sharply reducing production levels. Therefore, the ability to tightlycontrol protein expression, as described for regulated gene therapy,permits cells to be grown to high density in the absence of proteinproduction. Only after an optimum cell density is reached, is expressionof the gene activated and the protein product subsequently harvested.

A similar problem is encountered in the construction and use of“packaging lines” for the production of recombinant viruses forcommercial (e.g., gene therapy) and experimental use. These cell linesare engineered to produce viral proteins required for the assembly ofinfectious viral particles harboring defective recombinant genomes.Viral vectors that are dependent on such packaging lines includeretrovirus, adenovirus, and adeno-associated virus. In the latter case,the titer of the virus stock obtained from a packaging line is directlyrelated to the level of production of the viral rep and core proteins.But these proteins are highly toxic to the host cells. Therefore, it hasproven difficult to generate high-titer recombinant viruses. Thisinvention provides a solution to this problem, by allowing theconstruction of packaging lines in which the rep and core genes areplaced under the control of regulatable transcription factors of thedesign described here. The packaging cell line can be grown to highdensity, infected with helper virus, and transfected with therecombinant viral genome. Then, expression of the viral proteins encodedby the packaging cells is induced by the addition of dimerizing agent toallow the production of virus at high titer.

E. Use of chimeric DBDs as genomic labelling reagents. Chimeric proteinscontaining a composite DNA binding region can be used to labelrecognized nucleotide sequences in DNA molecules, including whole genomepreparations such as chromosome spreads and immobilized DNA matrices,that contain the specific recognition sites. This approach may be usedfor localizing these sequences to specific chromosomal regions aftertheir introduction into genomic DNA, for example in a retroviral vectorfor a gene therapy application. More generally, chimeric proteinscontaining a composite DNA binding region may be used as reagents toreveal the location of their nucleotide recognition sites forapplications such as gene mapping, where they may be used as cytogeneticmarkers. DNA binding by composite DNA binding regions may haveadvantages over techniques such as fluoresence in situ hybridization(FISH) in that shorter nucleotide sequences could be specificallyrecognized. These approaches require the chimeric protein to be labelledin a way, for example by tagging with an epitope such asglutathione-S-transferase (GST) or the haemagglutinin (HA) tag, that canbe readily visualized, e.g. by immunological and colorimetric detection;by biotinylation followed by detection with streptavidin; or by fusionto a directly detectable moiety such as green fluorescent protein (GFP).

F. Biological research. This invention is applicable to a wide range ofbiological experiments in which precise recognition of a target gene isdesired. These include: (1) expression of a protein or RNA of interestfor biochemical purification; (2) regulated expression of a protein orRNA of interest in tissue culture cells for the purposes of evaluatingits biological function; (3) regulated expression of a protein or RNA ofinterest in transgenic animals for the purposes of evaluating itsbiological function; (4) regulating the expression of another regulatoryprotein that acts on an endogenous gene for the purposes of evaluatingthe biological function of that gene. Transgenic animal models and otherapplications in which the composite DNA-binding domains of thisinvention may be used include those disclosed in U.S. patent applicationSer. Nos. 08/292,595 and 08/292,596 (filed Aug. 18, 1994).

G. Kits. This invention further provides kits useful for the foregoingapplications. One such kit contains a first DNA sequence encoding achimeric protein comprising a composite DNA binding region of thisinvention (and may contain additional domains as discussed above) and asecond DNA sequence containing a target gene linked to a DNA sequence towhich the chimeric protein is capable of binding. Alternatively, thesecond DNA sequence may contain a cloning site for insertion of adesired target gene by the practitioner. For regulatable applications,i.e., in cases in which the recombinant protein contains a compositeDNA-binding domain and a receptor domain, the kit may further contain athird DNA sequence encoding a transcriptional activating domain and asecond receptor domain, as discussed above. Such kits may also contain asample of a dimerizing agent capable of dimerizing the two recombinantproteins and activating transcription of the target gene.

The following examples contain important additional information,exemplification and guidance which can be adapted to the practice ofthis invention in its various embodiments and the equivalents thereof.The examples are offered by way illustration and not by way limitation.

EXAMPLES

The following examples describe the design, construction and use ofchimeric proteins containing a composite DNA-binding region,identification of a consensus nucleic acid sequence bound by thecomposite DNA-binding region, assessment of its binding specificity anddemonstration of its in vivo activity. The teachings of references citedherein are hereby incorporated by reference.

Example 1 Computer Modeling

Computer modeling studies (PROTEUS and MOGLI) were used to visualize howzinc fingers might be fused to the Oct-1 homeodomain. The known crystalstructures of the Zif268 DNA (Pavletich and Pabo, Science 252:809(1991)) and Oct-1-DNA (Klemm, et al., Cell 77:21 (1994)) complexes werealigned by superimposing phosphates of the double helices in severaldifferent orientations. This study yielded two arrangements whichappeared to be suitable for use in a chimeric protein.

Each model was constructed by juxtaposing portions of two differentcrystallographically determined protein-DNA complexes. Models wereinitially prepared by superimposing phosphates of the double helices invarious registers and were analyzed to see how the polypeptide chainsmight be connected. Superimposing sets of phosphates typically gave rootmean squared distances of 0.5-1.5 Å between corresponding atoms. Thesedistance gave some perspective on the error limits involved in modeling,and uncertainties about the precise arrangements were one of the reasonsfor using a flexible linker containing several glycines.

In one alignment, the carboxyl-terminal region of zinc finger 2 was 8.8Å away from the amino-terminal region of the homeodomain, suggestingthat a short polypeptide linker could connect these domains. In thismodel, the chimeric protein would bind a hybrid DNA site with thesequence 5′-AAATNNTGGGCG-3′ (SEQ ID NO.: 18). The Oct-1 homeodomainwould recognize the AAAT subsite, zinc finger 2 would recognize the TGGsubsite, and zinc finger 1 would recognize the GCG subsite. No risk ofsteric interference between the domains was apparent in this model.

The second plausible arrangement would also have a short polypeptidelinker connecting zinc finger 2 to the homeodomain (a distance of lessthan 10 Å); however, the subsites are arranged so that the predictedbinding sequence is 5′-CGCCCANNAAAT-3′ (SEQ ID NO.: 19). This model wasnot explicitly used in the subsequent studies, although it is possiblethat the flexible linker will also allow ZFHD1 to recognize this site.

Example 2 Construction of a Chimeric Protein

The design strategy was tested by construction of a chimeric protein,ZFHD1, that contained fingers 1 and 2 of Zif268, aglycine-glycine-arginine-arginine linker, and the Oct-1 homeodomain(FIG. 1A). A fragment encoding Zif268 residues 333-390 (Christy et al.,Proc. Natl. Acad. Sci. USA 85:7857 (1988)), two glycines and the Oct-1residues 378-439 (Sturm et al., Genes & Development 2:1582 (1988)) wasgenerated by polymerase chain reaction, confirmed by dideoxysequencing,and cloned into the BamHI site of pGEX2T (Pharmacia) to generate anin-frame fusion to glutathione S-transferase (GST). The GST-ZFHD1protein was expressed by standard methods (Ausubel et al., Eds., CURRENTPROTOCOLS IN MOLECULAR BIOLOGY (John Wiley & Sons, New York, 1994),purified on Glutathione Sepharose 4B (Pharmacia) according to themanufacturer's protocol, and stored at −80° C. in 50 mM Tris pH 8.0, 100mM KCl, and 10% glycerol. Protein concentration was estimated bydensitometric scanning of coomassie-stained SDS PAGE-resolved proteinsusing bovine serum albumin (Boehringer-Mannheim Biochemicals) asstandard. The DNA-binding activity of this chimeric protein wasdetermined by selecting binding sites from a random pool ofoligonucleotides.

Example 3 Consensus Binding Sequences

The probe used for random binding site selection contained the sequence5′-GGCTGAGTCTGAACGGATCCN₂₅CCTCGAG ACTGAGCGTCG-3′ (SEQ ID NO.: 22). Fourrounds of selection were performed as described in Pomerantz and Sharp,Biochemistry 33:10851 (1994), except that 100 ngpoly[d(I-C)]/poly[d(I-C)] and 0.025% Nonidet P-40 were included in thebinding reaction. Selections used 5 ng randomized DNA in the first roundand approximately 1 ng in subsequent rounds. Binding reactions contained6.4 ng of GST-ZFHD1 in round 1, 1.6 ng in round 2, 0.4 ng in round 3 and0.1 ng in round 4.

After four rounds of selection, 16 sites were cloned and sequenced (SEQID NOS.: 1-16, FIG. 1B). Comparing these sequences revealed theconsensus binding site 5′-TAATTANGGGNG-3′ (SEQ ID NO.: 17). The 5′ halfof this consensus, TAATTA, resembled a canonical homeodomain bindingsite TAATNN (Laughon, (1991)), and matched the site (TAATNA) that ispreferred by the Oct-1 homeodomain in the absence of the POU-specificdomain (Verrijzer et al., EMBO J 11:4993 (1992)). The 3′ half of theconsensus, NGGGNG, resembled adjacent binding sites for fingers 2 (TGG)and 1 (GCG) of Zif268. The guanines were more tightly conserved than theother positions in these zinc finger subsites, and the crystal structureshows that these are the positions of the critical side chain-baseinteractions (Pavletich and Pabo (1991)).

The consensus sequence of ZFHD1 was determined (5′-TAATTANGGGNG-3′, SEQID NO.: 17), but because of the internal symmetry of the TAATTA subsitethis sequence was consistent with the homeodomain binding in either oftwo orientations (FIG. 1C, compare mode 1 and mode 2). The secondarrangement (FIG. 1C, mode 2), in which the critical TAAT is on theother strand and directly juxtaposed with the zinc finger (TGGGCG)subsites, was considered unlikely since modeling suggested that thisarrangement required a linker to span a large distance between thecarboxyl-terminal region of finger 2 and the amino-terminal region ofthe homeodomain.

To determine how the homeodomain binds to the TAATTA sequence in the 5′half of the consensus, ZFHD1 was tested for binding to probes(5′-TAATGATGGGCG-3′, SEQ ID NO.: 21, and 5′-TCATTATGGGCG-3′, SEQ ID NO.:23) designed to distinguish between these orientations. ZFHD1 bound tothe 5′-TAATGATGGGCG-3′ (SEQ ID NO: 21) probe with a dissociationconstant of 8.4×10⁻¹⁰ M, and preferred this probe to the5′-TCATTATGGGCG-3′ (SEQ ID NO. 23) probe by a factor of 33. Thissuggests that the first four bases of the consensus sequence form thecritical TAAT subsite that is recognized by the homeodomain and thatZFHD1 binds as predicted in the model shown in mode 1 of FIG. 1C.

Example 4 Novel Specificity

ZFHD1, the Oct-1 POU domain (containing a homeodomain and a POU-specificdomain, Pomerantz et al., Genes & Development 6:2047 (1992)) and thethree zinc fingers of Zif268 (obtained from M. Elrod-Erickson) werecompared for their abilities to distinguish among the Oct-1 site5′-ATGCAAATGA-3′ (SEQ ID NO.: 20), the Zif268 site 5′-GCGTGGGCG-3′ andthe hybrid binding site 5′-TAATGATGGGCG-3′ (SEQ ID NO.: 21). DNA-bindingreaction contained 10 mM Hepes (pH 7.9), 0.5 mM EDTA, 50 mM KCl, 0.75 mMDTT, 4% Ficoll400, 300 μg/ml of bovine serum albumin, with theappropriate protein and binding site in a total volume of 10 μl. Theconcentration of binding site was always lower than the apparentdissociation constant by at least a factor of 10. Reactions wereincubated at 30° C. for 30 minutes and resolved in 4% nondenaturingpolyacrylamide gels. Apparent dissociation constants were determined asdescribed in Pomerantz and Sharp, Biochemistry 33:10851 (1994). Probeswere derived by cloning the following fragments into the Kpn I and Xho Isites of pBSKII+ (Stratagene) and excising the fragment with Asp718 andHind III:

(SEQ ID NO.: 24) 5′-CCTCGAGGTCATTATGGGCGCTAGGTACC-3′, (SEQ ID NO.: 25)5′-CCTCGAGGCGCCCATCATTACTAGGTACC-3′, (SEQ ID NO.: 26)5′-CCTCGAGGCGCCCACGCCTAGGTACC-3′, (SEQ ID NO: 27)5′-CCTCGAGGTCATTTGCATACTAGGTACC-3′.

The GST-ZFHD1 protein was titrated into DNA-binding reactions containingthe probes listed at the top of each set of lanes in FIG. 2. Lanes 1, 6,11 and 16 contained the protein at 9.8×10⁻¹¹ M, and proteinconcentration was increased in 3-fold increments in subsequent lanes ofeach set. The chimeric protein ZFHD1 preferred the optimal hybrid siteto the octamer site by a factor of 240 and did not bind to the Zif site.

The Oct-1-POU protein was titrated into DNA-binding reactions as withZFHD1, but lanes 1, 6, 11 and 16 contained the protein at 2.1×10⁻¹² M.The POU domain of Oct-1 bound to the octamer site with a dissociationconstant of 1.8×10⁻¹⁰ M, preferring this site to the hybrid sequences byfactors of 10 and 30, and did not bind to the Zif site.

A peptide containing Zif fingers 1, 2 and 3 was titrated intoDNA-binding reactions as with ZFHD1 and the Oct-1-POU protein with lanes1, 6, 11 and 16 containing the peptide at 3.3×10⁻¹¹ M. The three fingersof Zif268 bound to the Zif site with a dissociation constant of3.3×10⁻¹⁰ M, and did not bind to the other three sites. Theseexperiments show that ZFHD1 binds tightly and specifically to the hybridsite and displayed DNA-binding specificity that was clearly distinctfrom that of either of the original proteins.

Example 5 in vivo Activity

ZFHD1 was fused to a transcriptional activation domain, and transfectionexperiments were used to determine whether the novel DNA-binding proteincould function in vivo. An expression plasmid encoding ZFHD1 fused tothe carboxyl-terminal 81 amino acids of the Herpes Simplex Virus VP16protein (ZFHD1-VP16) was co-transfected into 293 cells with reporterconstructs containing the SV40 promoter and the firefly luciferase gene(FIG. 3). The 293 cells were co-transfected with 5 μg of reportervector, 10 μg of expression vector, and 5 μg of pCMV-hGH used as aninternal control. The reporter vectors contained two tandem copies ofeither the ZFHD1 site (TAATGATGGGCG), the Oct-1 site (ATGCAAATGA, SEQ IDNO: 20), the Zif site (GCGTGGGCG, SEQ ID NO: 21) or no insert.

The ZFHD1-VP16 expression vector was constructed by cloning a fragmentencoding ten amino acid polypeptide epitope MYPYDVPDYA; ZFHD1; and VP16residues 399-479 (Pellett et al., Proc. Natl. Acad. Sci. USA 82:5870(1985)) into the Not I and Apa I sites of Rc/CMV (Invitrogen). Reportervectors were constructed by cloning into the Xho I and Kpn I sites ofpGL2-Promoter (Promega) the following fragments:

(SEQ ID NO.: 28) 5′-GGTACCAGTATGCAAATGACTGCAGTATGCAAATGACCTCGAG-3′, (SEQID NO.: 29) 5′-GGTACCAGGCGTGGGCGCTGCAGGCGTGGGCGCCTCGAG-3′, (SEQ ID NO.:30) 5′-GGTACCAGTAATGATGGGCGCTGCAGTAATGATGGGCGCCTCGA G-3′.

The 293 cells were transfected using calcium phosphate precipitationwith a glycerol shock as described in Ausubel et al., Eds., CurrentProtocols in Molecular Biology (John Wiley & Sons, New York, (1994).Quantitation of hGH production was performed using the Tandem-R HGHImmunoradiometric Assay (Hybritech Inc., San Diego, Calif.) according tothe manufacturer's instructions. Cell extracts were made 48 hours aftertransfection and luciferase activity was determined using 10 μl of 100μl total extract/10 cm plate and 100 μl of Luciferase Assay Reagent(Promega) in a ML2250 Luminometer (Dynatech Laboratories, Chantilly,Va.) using the enhanced flash program and integrating for 20 secondswith no delay. The level of luciferase activity obtained, normalized tohGH production, was set to 1.0 for the co-transfection of Rc/CMV withthe no-insert reporter pGL2-Promoter.

To determine whether the chimeric protein could specifically regulategene expression, reporter constructs containing two tandem copies ofeither the ZFHD1 site 5′-TAATGATGGGCG-3′, the octamer site5′-ATGCAAATGA-3′ (SEQ ID NO: 20) or the Zif site 5′-GCGTGGGCG-3′ (SEQ IDNO: 21) inserted upstream of the SV40 promoter were tested. When thereporter contained two copies of the ZFHD1 site, the ZFHD1-VP16 proteinstimulated the activity of the promoter in a dose-dependent manner.Furthermore, the stimulatory activity was specific for the promotercontaining the ZFHD1 binding sites. At levels of protein whichstimulated this promoter by 44-fold, no stimulation above background wasobserved for promoters containing the octamer or Zif sites. Thus, ZFHD1efficiently and specifically recognized its target site in vivo.

Example 6 Additional Examples

The following additional examples illustrate chimeric proteinscontaining the composite DNA-binding domain ZFHD1 together with variousother domains, and the use of these chimeras in constitutive andligand-dependent transcriptional activation.

A. Plasmids

pCGNNZFHD1

An expression vector for directing the expression of ZFHD1 codingsequence in mammalian cells was prepared as follows. Zif268 sequenceswere amplified from a cDNA clone by PCR using primers 5′Xba/Zif and3′Zif+G. Oct1 homeodomain sequences were amplified from a cDNA clone byPCR using primers 5′Not Oct HD and Spe/Bam 3′Oct. The Zif268 PCRfragment was cut with XbaI and NotI. The Oct1 PCR fragment was cut withNotI and BamHI. Both fragments were ligated in a 3-way ligation betweenthe XbaI and BamHI sites of pCGNN (Attar and Gilman, 1992) to makepCGNNZFHD1 in which the cDNA insert is under the transcriptional controlof human CMV promoter and enhancer sequences and is linked to thenuclear localization sequence from SV40 T antigen. The plasmid pCGNNalso contains a gene for ampicillin resistance which can serve as aselectable marker.

pCGNNZFHD1-p65

An expression vector for directing the expression in mammalian cells ofa chimeric transcription factor containing the composite DNA-bindingdomain, ZFHD1, and a transcription activation domain from p65 (human)was prepared as follows. The sequence encoding the C-terminal region ofp65 containing the activation domain (amino acid residues 450-550) wasamplified from pCGN-p65 using primers p65 5′ Xba and p65 3′ Spe/Bam. ThePCR fragment was digested with Xba1 and BamH1 and ligated between theSpe1 and BamH1 sites of pCGNN ZFHD1 to form pCGNN ZFHD-p65AD.

The P65 transcription activation sequence contains the following linearsequence:

(SEQ ID NO: 34) CTGGGGGCCTTGCTTGGCAACAGCACAGACCCAGCTGTGTTCACAGACCTGGCATCCGTCGACAACTCCGAGTTTCAGCAGCTGCTGAACCAGGGCATACCTGTGGCCCCCCACACAACTGAGCCCATGCTGATGGAGTACCCTGAGGCTATAACTCGCCTAGTGACAGGGGCCCAGAGGCCCCCCGACCCAGCTCCTGCTCCACTGGGGGCCCCGGGGCTCCCCAATGGCCTCCTTTCAGGAGATGAAGACTTCTCCTCCATTGCGGACATGGACTTCTCAGCCCTGCTGAGTCAGATC AGCTCCpCGNNZFHD1-FKBPx3

An expression vector for directing the expression of ZFHD1 linked tothree tandem repeats of human FKBP was prepared as follows. Three tandemrepeats of human FKBP were isolated as an XbaI-BamHI fragment frompCGNNF3 and ligated between the Spe1 and BamHI sites of pCGNNZFHD1 tomake pCGNNZFHD1-FKBPx3 (ATCC Accession No. 97399).

pZHWTx8SVSEAP

A reporter gene construct containing eight tandem copies of a ZFHD1binding site (Pomerantz et al., 1995) and a gene encoding secretedalkaline phosphatase (SEAP) was prepared by ligating the tandem ZFHD1binding sites between the Nhe1 and BglII sites of pSEAP-Promoter Vector(Clontech) to form pZHWTx8SVSEAP. The ZHWTx8SEAP reporter contains twocopies of the following sequence in tandem:

(SEQ ID NO: 35) CTAGCTAATGATGGGCGCTCGAGTAATGATGGGCGGTCGACTAATGATGGGCGCTCGAGTAATGATGGGCGTThe ZFHD1 binding sites are underlined.pCGNN F1 and F2

One or two copies of FKBP12 were amplified from pNF3VE using primersFKBP 5′ Xba and FKBP 3′ Spe/Bam. The PCR fragments were digested withXba1 and BamH1 and ligated between the Xba1 and BamH1 sites of pCGNNvector to make pCGNN F1 or pPCGNN F2. pCGNNZFHD1-FKBPx3 can serve as analternate source of the FKBP cDNA.

pCGNN F3

A fragment containing two tandem copies of FKBP was excised from pCGNNF2 by digesting with Xba1 and BamH1. This fragment was ligated betweenthe Spe1 and BamH1 sites of pCGNN F1.

pCGNN F3VP16

The C-terminal region of the Herpes Simplex Virus protein, VP16 (AA418-490) containing the activation domain was amplified frompCG-Gal4-VP16 using primers VP16 5′ Xba and VP16 3′ Spe/Bam. The PCRfragment was digested with Xba1 and BamH1 and ligated between the Spe1and BamH1 sites of pCGNN F3 plasmid.

pCGNN F3p65

The Xba1 and BamH1 fragment of p65 containing the activation domain wasprepared as described above. This fragment was ligated between the Spe1and BamH1 sites of pCGNN F3.

B. Primers

5′Xba/Zif (SEQ ID NO: 36) 5′ATGCTCTAGAGAACGCCCATATGCTTGCCCT 3′Zif + G(SEQ ID NO: 37) 5′ATGCGCGGCCGCCGCCTGTGTGGGTGCGGATGTG 5′Not OctHD (SEQ IDNO: 38) 5′ATGCGCGGCCGCAGGAGGAAGAAACGCACCAGC Spe/Bam 3′Oct (SEQ ID NO:39) 5′GCATGGATCCGATTCAACTAGTGTTGATTCTTTTTTCTTTCTGGCGGC G FKBP 5′Xba (SEQID NO: 40) 5′TCAGTCTAGAGGAGTGCAGGTGGAAACCAT FKBP 3′ Spe/Bam (SEQ ID NO:41) A5′TCAGGGATCCTCAATAACTAGTTTCCAGTTTTAGAAGCTC VP16 5′ Xba (SEQ ID NO:42) 5′ACTGTCTAGAGTCAGCCTGGGGGACGAG VP16 3′ Spe/Bam (SEQ ID NO: 43)5′GCATGGATCCGATTCAACTAGTCCCACCGTACTCGTCAATTCC P65 5′ Xba (SEQ ID NO: 44)5′ATGCTCTAGACTGGGGGCCTTGCTTGGCAAC p65 3′ Spe/Bam (SEQ ID NO: 45)5′GCATGGATCCGCTCAACTAGTGGAGCTGATCTGACTCAGC. Dimerizing Agent

FK1012 consists of two molecules of the natural product FK506 covalentlyjoined to one another by a synthetic linker and can be prepared fromFK506 using published procedures. See e.g. PCT/US94/01617 and Spencer etal, 1993. FK1012 is capable of binding to two FKBP domains andfunctioning as a dimerizing agent for FKBP-containing chimeric proteins.

(i) ZFHD1-p65 and ZFHD1-VP16 Chimeric Proteins Activate Transcription ofa Target Gene Linked to a Nucleotide Sequence Containing ZFHD1 BindingSites.

HT1080 cells were grown in MEM (GIBCO BRL) supplemented with 10% FetalBovine Serum. Cells in 35 mm dishes were transiently transfected bylipofection as follows: 10, 50, 250 ng of ZFHD-activation domain fusionplasmids together with 1 μg of pZHWTx8SVSEAP plasmid DNA were added to amicrofuge tube with pUC118 plasmid to a total of 2.5 μg DNA per tube.The DNA in each tube was then mixed with 20 μg lipofectamine in 200 μlOPTIMEM (GIBCO BRL). The DNA-lipofectamine mix was incubated at roomtemperature for 20 min. Another 800 μl of OPTIMEM was added to eachtube, mixed and added to HT1080 cells previously washed with 1 ml DMEM(GIBCO BRL). The cells were incubated at 37° C. for 5 hrs. At this time,the DNA-lipofectamine media was removed and the cells were refed with 2ml MEM containing 10% Fetal Bovine Serum. After 24 hrs incubation at 37°C., 20 μl of media was removed and assayed for SEAP activity asdescribed (Spencer et al., 1993).

Results

Both ZFHD1-VP16 and ZFHD1-p65 support transcriptional activation of agene encoding SEAP linked to ZFHD1 binding sites. The results are shownin FIG. 4A.

(ii) FK1012-Dependent Transcriptional Activation with ZFHD1-FKBPx3 andFKBPx3-VP16 or FKBPx3-p65

293 cells were grown in D-MEM (Gibco BRL) supplemented with 10% BovineCalf Serum. Cells in 35 mm dishes (2.5×10⁵ cells/dish) were transientlytransfected with use of calcium phosphate precipitation (Ausubel et.al., 1994). Each dish received 375 ng pZHWTx8SVSEAP; 12 ngpCGNNZFHD1-FKBPx3 and 25 ng pCGNNFKBPx3-VP16 or pCGNNFKBPx3-p65.Following transfection, 2 ml fresh media was added and supplemented withFK1012 to the desired concentration. After a 24 hour incubation 100 mlaliquot of media was removed and assayed for SEAP activity as described(Spencer et. al., 1993).

Results

ZFHD1-FKBPx3 supports FK1012 dependent transcriptional activation inconjunction with FKBPx3VP16 or FKBPx3-p65. Peak activation was observedat FK1012 concentration of 100 nM. See FIG. 4B.

(iii) Synthetic Dimerizer-Dependent Transcriptional Activation withZFHD1-FKBPx3 and FKBPx3-VP16 or FKBPx3-p65

An analgoous experiment was conducted using a wholly synthetic dimerizerin place of FK1012. Like FK1012, the synthetic dimerizer is a divalentFKBP-binder and is capable of dimerizing chimeric proteins which containFKBP domains. In this experiment, 293 cells were grown in DMEMsupplemented with 10% Bovine Calf Serum. Cells in 10 cm dishes weretransiently transfected by calcium phosphate precipitation (Natesan andGilman, 1995, Mol. Cell Biol, 15, 5975-5982). Each plate received 1 μgof pZHWTx8SVSEAP reporter, 50 ng pCGNNZFHD1-FKBP3x3, 50 ng pCGNNF3p65 orpCGNNF3VP16. Following transfection, 2 ml fresh media was added andsupplemented with a synthetic dimerizer to the desired concentration.After 24 hrs, 100 μl of the media was assayed for SEAP activity asdescribed (Spencer et al, 1993).

Results

ZFHD1-FKBPx3 supports synthetic dimerizer-dependent transcriptionalactivation in conjunction with FKBPx3-VP16 or FKBPx3-p65. See FIG. 4C.

REFERENCES

-   1. Attar, R. M., and M. Z. Gilman 1992. Mol. Cell. Biol.    12:2432-2443-   2. Ausubel, F. M. et al., Eds., 1994. CURRENT PROTOCOLS IN MOLECULAR    BIOLOGY (Wiley, NY)-   3. Pomerantz, J. L., et al. 1995. Science. 267:93-96.-   4. Spencer, D. M., et al. 1993. Science. 262:1019-1024.

Example 7 Rapamycin-Dependent Transcriptional Activation withZFHD1-FKBPx3 and FRAP-p65 in Whole Animals

Using the approach described in Example 6, constructs were preparedencoding the ZFHD1-FKBPx3 fusion protein, a second fusion proteincontaining the FKBP:rapaymcin binding (“FRB”) region of FRAP linked tothe p65 activation domain, and a reporter cassette containing a geneencoding human growth hormone linked to multiple ZFHD1 binding sites.The natural product, rapamycin, forms a ternary complex with FKBP12 andFRAP. Similarly, rapamycin is capable of binding to one or more of theFKBP domains and FRAP FRB domains of the fusion proteins. The threeconstructs were introduced into HT1080 cells which were then shown tosupport rapamycin-dependent expression of the hGH gene in cell culture,analogously to the experiments described in Example 6.

2×10⁶ cells from the transfected HT1080 culture were administered tonu/nu mice by intramuscular injection. Following cell implantation,rapamycin was administered i.v. over a range of doses (from 10-10,000μg/kg). Serum samples were collected from the mice 17 hours afterrapamycin administration. Control groups consisted of mice that receivedno cells but 1.0 mg/kg rapamycin (i.v.) as well as mice that receivedthe cells but no rapamycin.

Dose-responsive expression of hGH was observed (as circulating hGH) overthe range of rapamycin doses administered. Neither control groupproduced measurable hGH. The limit of detection of the hGH assay is0.0125 ng/ml. See FIG. 5.

These data show functional DNA binding of ZFHD1-FKBP(x3) to a ZFHD1binding site in the context of dimerization with another fusion proteinin whole animals. These data demonstrate that in vivo administration ofa dimerizing agent can regulate gene expression in whole animals ofsecreted gene products from cells containing the fusion proteins and aresponsive target gene cassette. We have previously demonstrated that abolus hGH administration, either i.p. or i.v., results in rapid hGHclearance with a half-life of less than 2 minutes and undetectablelevels by 30 minutes. Therefore, the observed hGH secretion in thisexample appears to be a sustained phenomenon.

Example 8 FRAP FRB Constructs

This Example provides further background and information relevant toconstructs encoding chimeric proteins containing an FRB domain derivedfrom FRAP for use in the practice of this invention. The VP16-FRBconstruct described below is analogous to the p65-FRB construct usedExample 7.

Rapamycin is a natural product which binds to a FK506-binding protein,FKBP, to form a rapamycin:FKBP complex. That complex binds to theprotein FRAP to form a ternary, [FKBP:rapamycin]:[FRAP], complex. Therapamycin-dependent association of FKBP12 and a 289 kDa mammalianprotein termed FRAP, RAFT1 or RAPT1 and its yeast homologs DRR and TOR(hereafter referred to as “FRAP”) have been described by severalresearch groups. See e.g. Brown et al, 1994, Nature 369:756-758,Sabatini et al, 1994, Cell 78:35-43, Chiu et al, 1994, Proc. Natl. Acad.Sci. USA 91:12574-12578, Chen et al, 1994, Biochem. Biophys. Res. Comm.203:1-7, Kunz et al, 1993 Cell 73:585-596, Cafferkey et al, 1993 Mol.Cell. Biol. 13:6012-6023. Chiu et al, supra, and Stan et al, 1994, J.Biol. Chem. 269:32027-32030 describe the rapamycin-dependent binding ofFKBP12 to smaller subunits of FRAP.

Construct Encoding FRAP Domain(s)-VP16 Transcriptional ActivationDomain(s)-Epitope Tag.

The starting point for assembling this construct was the eukaryoticexpression vector pBJ5/NF1E, described in PCT/US94/01617. pBJ5 is aderivative of pCDL-SR (MCB 8, 466-72) in which a polylinker containing5′ SacII and 3′ EcoRI sites has been inserted between the 16S splicesite and the poly A site. To construct pBJ5/NF1E a cassette was clonedinto this polylinker that contained a Kozak sequence and start site, thecoding sequence of the SV40 T antigen nuclear localization sequence(NLS), a single FKBP domain, and an epitope tag from the H. influenzahaemagglutinin protein (HA), flanked by restriction sites as shownbelow:

   Kozak        SV40 NLS                       FKBP(5′)         M E D PK K K R K V L E G V Q V E . . .CCGCGGCCACCATGCTCGACCCTAAGAAGAAGAGAAAGGTACTCGAGGGCGTGCAGGTGGAG . . .SacII      (X/S)                             XhoI       FKBP(3′)             HA(flu)tag              . . . L L K L E V DY P Y D V P D Y A E D End (SEQ ID NO: 47) . ..CTTCTAAAACTGGAAGTCGACTATCCGTACGACGTACCAGACTACGCACTCGACTAAGAATTC (SEQ IDNO: 46)                    SalI                             (X/S)  EcoRIwhere (X/S) denotes the result of a ligation event between thecompatible products of digestion by XhoI and SalI, to produce a sequencethat is cleavable by neither enzyme. Thus the XhoI and SalI sites thatflank the FKBP coding sequence are unique.

The series of constructs encoding FRAP-VP16 fusions is assembled frompBJ5/NF1E in two steps: (i) the XhoI-SalI restriction fragment encodingFKBP is excised and replaced with fragments encompassing all or part ofthe coding sequence of human FRAP, obtained by PCR amplification,generating construct NR1E and relatives (where R denotes FRAP or aportion thereof; (ii) the coding sequence of the VP16 activation domainis cloned into the unique SalI site of these vectors to yield constructNR1V1E and relatives. At each stage additional manipulations areperformed to generate constructs encoding multimers of the FRAP-derivedand/or VP16 domains.

(i) Portions of human FRAP that include the region required for FRAPbinding are amplified by PCR using a 5′ primer that contains a XhoI siteand a 3′ primer that contains a SalI site. The amplified region canencode full-length FRAP (primers 1 and 4: fragment a); residues 2012through 2144 (a 133 amino acid region that retains the ability to bindFKBP-rapamycin; see Chiu et al. (1994) Proc. Natl. Acad. Sci. USA 91:12574-12578) (primers 2 and 5: fragment b); or residues 2025 through2114 (a 90 amino acid region that also retains this ability; see Chen etal. (1995) Proc. Natl. Acad. Sci. USA 92: 4947-4951)(primers 3 and 6:fragment c). The DNA is amplified from human cDNA or a plasmidcontaining the FRAP gene by standard methods, and the PCR product isisolated and digested with SalI and XhoI. Plasmid pBJ5/NF1E is digestedwith SalI and XhoI and the cut vector purified. The digested PCRproducts are ligated into the cut vector to produce the constructsNRa1E, NRb1E and NRc1E, where Ra, Rb and Rc denote the full-length orpartial FRAP fragments as indicated above. The constructs are verifiedby DNA sequencing.

Multimers of the FRAP domains are obtained by isolating the Ra, Rb or Rcsequences from the NRa1E, NRb1E and NRc1E vectors as XhoI/SalI fragmentsand then ligating these fragments back into the parental constructlinearized with XhoI. Constructs containing two, three or more copies ofthe FRAP domain (designated NRa2E, NRa3E, NRb2E, NRb3E etc) areidentified by restriction or PCR analysis and verified by DNAsequencing.

5′ ends of amplified products: FRAP fragment a (full-length: primer 1)         L E L G T G P A A (SEQ ID NO: 49)5′ CGAGTCTCGAGCTTGGAACCGGACCTGCCGCC (SEQ ID NO: 48)         XhoI FRAPfragment b (residues 2012-2144: primer 2)         L E V S E E L I R (SEQID NO: 51) 5′ CGAGTCTCGAGGTGAGCGAGGAGCTGATCCGA (SEQ ID NO: 50)        XhoI FRAP fragment c (residues 2025-2114: primer 3)          L EE M W H E G L (SEQ ID NO: 53) 5′ CGAGTCTCGAGGAGATGTGGCATGAAGGCCTG (SEQID NO: 52)         XhoI 3′ ends of amplified products: FRAP fragment a(full-length: primer 4)    I G W C P F W V D (SEQ ID NO: 55)5′ ATTGGCTGGTGCCCTTTCTGGGTCGACCGAGT (SEQ ID NO: 54)3′ TAACCGACCACGGGAAAGACCCAGCTGGCTCA              SalI FRAP fragment b(residues 2012-2144: primer 5)    L A V P G T Y V D (SEQ ID NO: 57)5′ TTGGCTGTGCCAGGAACATATGTCGACCGAGT (SEQ ID NO: 56)3′ AACCGACACGGTCCTTGTATACAGCTGGCTCA              SalI FRAP fragment c(residues 2012-2144: primer 6)    F R R I S K Q V D (SEQ ID NO: 59)5′ TTCCGACGAATCTCAAAGCAGGTCGACCGAGT (SEQ ID NO: 58)3′ AAGGCTGCTTAGAGTTTCGTCCAGCTGGCTCA              SalI

(ii) The VP16 transcriptional activation domain (amino acids 413-490) isamplified by PCR using a 5′ primer (primer 7) containing a XhoI site anda 3′ primer (primer 8) containing a SalI site. The PCR product isisolated, digested with SalI and XhoI, and ligated into plasmidpBJ5/NF1E digested with SalI and XhoI to generate the intermediate NV1E.The construct is verified by restriction or PCR analysis and DNAsequencing. Multimerized VP16 domains are created by isolating thesingle VP16 sequence as a XhoI-SalI fragment from NV1E, and thenligating this fragment back into NV1E that is linearized with XhoI. Thisprocess generates constructs NV2E, NV3E and NV4E etc which can beidentified by restriction or PCR analysis and verified by DNAsequencing.

5′ end of PCR product;                 413          L E A P P T D V (SEQID NO: 61) 5′ CGACACTCGAGGCCCCCCCGACCGATGTC (SEQ ID NO: 60)         XhoI3′ end of PCR product:                490    D E Y G G V D (SEQ ID NO:63) 5′ GACGAGTACGGTGGGGTCGACTGTCG (SEQ ID NO: 62)3′ CTGCTCATGCCACCCCAGCTGACAGC                      SalIThe final constructs encoding fusions of portions of FRAP with VP16 arecreated by transferring the VP16 sequences into the series ofFRAP-encoding vectors described in (i). XhoI-SalI fragments encoding the1, 2, 3 and 4 copies of the VP16 activation domains are generated bydigestion of NV1E, NV2E, NV3E and NV4E. These fragments are then ligatedinto vectors NRa1E, NRb1E and NRc1E linearized with SalI, generatingNRa1V1E, NRb1V1E, NRc1V1E, NRa1V2E, NRb1V2E, etc. Similarly, vectorsencoding multiple copies of the FRAP domains are obtained by ligation ofthe same fragments into vectors NRa2E, NRa3E, NRb2E, NRb3E etc. All ofthese vectors are identified by restriction or PCR analysis and verifiedby DNA sequencing. Thus the final series of vectors encodes (from the Nto the C terminus) a nuclear localization sequence, one or moreFRAP-derived domains fused N-terminally to one or more VP16transcriptional activation domains (contained on a single XhoI-SalIfragment), and an epitope tag.Oligonucleotides:

(SEQ ID NO: 48) 1 5′ CGAGTCTCGAGCTTGGAACCGGACCTGCCGCC (SEQ ID NO: 50) 25′ CGAGTCTCGAGGTGAGCGAGGAGCTGATCCGA (SEQ ID NO: 52) 35′ CGAGTCTCGAGGAGATGTGGCATGAAGGCCTG (SEQ ID NO: 54) 45′ ACTCGGTCGACCCAGAAAGGGCACCAGCCAAT (SEQ ID NO 56) 55′ ACTCGGTCGACATATGTTCCTGGCACAGCCAA (SEQ ID NO: 58) 65′ ACTCGGTCGACCTGCTTTGAGATTCGTCGGAA (SEQ ID NO: 60) 75′ CGACACTCGAGGCCCCCCCGACCGATGTC (SEQ ID NO: 62) 85′ CGACAGTCGACCCCACCGTACTCGTCSequence of representative final construct (NRc1V1E):

   Kozak     SV40 NLS                         FRAP(2025-2114)         ME D P K K K R K V L E E M W H E. . .CCGCGGCCACCATGCTCGACCCTAAGAAGAAGAGAAAGGTACTCGAGGAGATGTGGCATGAA . . .SacII      (X/S)                            XhoIFRAP(2025-2114)            VP16(413-490) . . . VP16(413-490)  _ . . . RI S K Q V D A P P T D  D E Y G G V D_CGAATCTCAAAGCAGGTCGAGGCCCCCCCGACCGAT_GACGAGTACGGTGGGGTCGAC          (S/X)               SalIHA(flu)tag  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Y P Y D V P D Y A E D End(SEQ ID NO: 65) TATCCGTACGACGTACCAGACTACGCACTCGACTAAGAATTC (SEQ ID NO:64)                           (X/S) EcoRI

Example 9 Constructs for Chimeric Proteins Containing AlternativeComposite DNA-binding Regions

The following DNA vectors were prepared containing recombinant DNAsequences encoding component DNA binding subdomains and composite DNAbinding regions containing them.

Constructs.

All plasmids are constructed in pET-19BHA, a pET-19B based vectormodified such that all expressed proteins contain an amino-terminalHistidine “Tag” for purification and an epitope tag forimmunoprecipitation. pET-19B is a well-known vector for expression ofheterologous proteins in E coli or in reticulocyte lysates.

Zinc Finger Constructs

All zinc finger sequences are derived from the human cDNA encodingSRE-ZBP (Attar, R. M. and Gilman, M. Z. 1992. MCB 12: 2432-2443).

p19B2F: Contains SREZBP zinc fingers 6 and 7 (amino acids 328 to 410)fused in frame to the epitope tag in p19BHA. DNA encoding ZBP zincfingers 6 and 7 was generated by PCR using primers 2F-Xba5′ andZNF-Spe/Bam (see below). The resulting fragment was cut with XbaI andBamHI and ligated between the XbaI and BamHI sites of pET-19BHA.p19B4F: Contains SREZBP zinc fingers 4, 5, 6 and 7 (amino acids 300 to410) fused in frame to the epitope tag in p19BHA. A DNA fragmentencoding ZBP zinc fingers 4, 5, 6 and 7 was generated by PCR usingprimers 4F-Xba5′ and ZNF-Spe/Bam. The resulting fragment was cut withXbaI and BamHI and ligated between the XbaI and BamHI sites ofpET-19BHA.p19B7F: Contains SREZBP zinc fingers 1 to 7 (amino acids 216 to 410)fused in frame to the epitope tag in p19BHA. DNA encoding ZBP zincfingers 1 to 7 was generated by PCR using primers 7F-Xba5′ andZNF-Spe/Bam. The resulting fragment was cut with XbaI and BamHI andligated between the XbaI and BamHI sites of pET-19BHA.p19BF1: Contains SREZBP zinc finger 1 (amino acids 204 to 241) fused inframe to the epitope tag in p19BHA. DNA encoding ZBP zinc finger 1 wasgenerated by PCR using primers ZBPZF15′ and ZBPZF13′. The resultingfragment was cut with XbaI and BamHI and ligated between the XbaI andBamHI sites of pET-19BHA.p19BF123: Contains SREZBP zinc fingers 1, 2 and 3 (amino acids 204 to297) fused in frame to the epitope tag in p19BHA. DNA encoding ZBP zincfingers 1, 2 and 3 was generated by PCR using primers ZBPZF15′ andZBPZF33′. The resulting fragment was cut with XbaI and BamHI and ligatedbetween the XbaI and BamHI sites of pET-19BHA.Homeodomain Constructp19BHH: Contains the Phox1 homeodomain and flanking amino acids (aminoacids 43 to 150 (Grueneberg et al. 1992. Science. 257: 1089-1095)) fusedin frame to the epitope tag in p19BHA. DNA encoding the Phox1 fragmentwas generated by PCR using primers Phox HH5′ Primer and Phox HH Spe/Bam.The resulting fragment was cut with XbaI and BamHI and ligated betweenthe XbaI and BamHI sites of pET-19BHA.Zinc Finger/Homeodomain Constructsp19B2FHH: Contains SREZBP zinc fingers 6 and 7 (amino acids 328 to 410)fused in frame to the epitope tag in p19BHA followed by the Phox1homeodomain (amino acids 43 to 150). An XbaI-BamHI fragment from p19BHHcontaining sequences encoding the Phox1 homeodomain was ligated betweenthe SpeI and BamHI sites of p19B2F.p19B4FHH: Contains SREZBP zinc fingers 4, 5, 6 and 7 (amino acids 300 to410) fused in frame to the epitope tag in p19BHA followed by the Phox1homeodomain (amino acids 43 to 150). An XbaI-BamHI fragment from p19BHHcontaining sequences encoding the Phox1 homeodomain was ligated betweenthe SpeI and BamHI sites of p19B4F.p19B7FHH: Contains SREZBP zinc fingers 1 to 7 (amino acids 216 to 410)fused in frame to the epitope tag in p19BHA followed by the Phox1homeodomain (amino acids 43 to 150). An XbaI-BamHI fragment from p19BHHcontaining sequences encoding the Phox1 homeodomain was ligated betweenthe SpeI and BamHI sites of p19B7F.p19BZF1HH: Contains SREZBP zinc finger 1 (amino acids 204 to 241) fusedin frame to the epitope tag in p19BHA followed by the Phox1 homeodomain(amino acids 43 to 150). An XbaI-BamHI fragment from p19BHH containingsequences encoding the Phox1 homeodomain was ligated between the SpeIand BamHI sites of p19BZF1.p19BZF123HH: Contains SREZBP zinc finger 1, 2 and 3 (amino acids 204 to297) fused in frame to the epitope tag in p19BHA followed by the Phox1homeodomain (amino acids 43 to 150). An XbaI-BamHI fragment from p19BHHcontaining sequences encoding the Phox1 homeodomain was ligated betweenthe SpeI and BamHI sites of p19BZF123.Homeodomain/Zinc Finger Constructsp19BHH2F: Contains Phox1 homeodomain (amino acids 43 to 150) fused inframe to the epitope tag in p19BHA followed by ZBP zinc fingers 6 and 7(amino acids 328 to 410). An XbaI-BamHI fragment from p19B2F containingsequences encoding ZBP zinc fingers 6 and 7 was ligated between the SpeIand BamHI sites of p19BHH.p19BHH4F: Contains Phox1 homeodomain (amino acids 43 to 150) fused inframe to the epitope tag in p19BHA followed by ZBP zinc fingers 4, 5, 6and 7 (amino acids 300 to 410). An XbaI-BamHI fragment from p19B4Fcontaining sequences encoding ZBP zinc fingers 4, 5, 6 and 7 was ligatedbetween the SpeI and BamHI sites of p19BHH.

p19BHH7F: Contains Phox1 homeodomain (amino acids 43 to 150) fused inframe to the epitope tag in p19BHA followed by ZBP zinc fingers 1 to 7(amino acids 216 to 410). An XbaI-BamHI fragment from p19B7F containingsequences encoding ZBP zinc fingers 1 to 7 was ligated between the SpeIand BamHI sites of p19BHH.

p19BHHZF1: Contains Phox1 homeodomain (amino acids 43 to 150) fused inframe to the epitope tag in p19BHA followed by ZBP zinc finger 1 (aminoacids 204 to 241). An XbaI-BamHI fragment from p19BZF1 containingsequences encoding ZBP zinc finger 1 was ligated between the SpeI andBamHI sites of p19BHH.p19BHHZF123: Contains Phox1 homeodomain (amino acids 43 to 150) fused inframe to the epitope tag in p19BHA followed by ZBP zinc fingers 1, 2 and3 (amino acids 204 to 297). An XbaI-BamHI fragment from p19BZF123containing sequences encoding ZBP zinc fingers 1, 2 and 3 was ligatedbetween the SpeI and BamHI sites of p19BHH.PCR Primers:

SRE-ZBP 2F-Xba5′: 5′-TCAGTCTAGATGTAACATATGCCAGAAAGCCTTC-3′ (SEQ ID NO:66) 4F-Xba5′: 5′-TCAGTCTAGATGCAAGGAGTGTGGAAAAACCTTT-3′ (SEQ ID NO: 67)7F-Xba5′: 5′-TCAGTCTAGATGTCATGAGTGTGGGAAAGCCTTT-3′ (SEQ ID NO: 68)ZNF-Spe/Bam: 5′-TCAGGGATCCTCAATAACTAGTAGCCAGTTTGTCTTTGTGGTGATA-3′ (SEQID NO: 69) ZBPZF15′: 5′-TCAGTCTAGACATAAGAAAGTCCTCTCTAG-3′ (SEQ ID NO:70) ZBPZF13′: 5′-TCAGGGATCCTCTATATCAACTAGTAGGCTTCTCACCAAGATGG-3′ (SEQ IDNO: 71) ZBPZF33′: 5′-TCAGGGATCCTCTATATCAACTAGTGGGCTCCTCCTGACTGTG-3′ (SEQID NO: 72) PHOX 1 Phox HH 5′ Primer: 5′-TCAGTCTAGAGGCCGGAGCCTGCTGGAGT-3′(SEQ ID NO: 73) Phox HH Spe/Bam:5′-TCAGGGATCCTCAATAACTAGTGTAGGATTTGAGGAGGGAA-3′ (SEQ ID NO: 74)

EQUIVALENTS

The invention disclosed herein is of broad applicability and issusceptible to many useful variations within the context described andillustrated herein. Those skilled in the art will recognize or be ableto ascertain from the foregoing disclosure, using no more than routineexperimentation, many valuable equivalents to the specific embodimentsof the invention described herein. Such equivalents are intended to beencompassed by the following claims.

1. A nucleic acid encoding a chimeric protein comprising a cleavagedomain and a composite nucleic acid-binding region, wherein thecomposite nucleic acid-binding region comprises at least two componentpolypeptide portions which are individually capable of binding specificnucleotide sequences, and wherein the at least two component polypeptideportions: (i) do not occur in the same protein in nature; (ii) do notoccur in the same protein in the order in which they are present in thechimeric protein; or (iii) do not occur in nature with the same spacingthat is present in the chimeric protein.
 2. The nucleic acid of claim 1,wherein at least one of the component polypeptide portions is a zincfinger module.
 3. The nucleic acid of claim 1, wherein the at least twocomponent polypeptide portions are zinc finger modules.
 4. The nucleicacid of claim 1, wherein at least one of the component polypeptideportions is a homeodomain.
 5. The nucleic acid of claim 2, wherein atleast one of the component polypeptide portions is a homeodomain. 6.The-nucleic acid of claim 1, wherein the chimeric protein is capable ofbinding a nucleotide sequence with a K_(d) value less than or equal to,or about, 10⁻⁸.
 7. The nucleic acid of claim 6, wherein the chimericprotein is capable of binding a DNA sequence with a K_(d) value lessthan or equal to, or about, 10⁻⁸.
 8. The nucleic acid of claim 6,wherein the chimeric protein is capable of binding an RNA sequence witha K_(d) value less than or equal to, or about, 10⁻⁸.
 9. The nucleic acidof claim 1, wherein the cleavage domain is a FokI cleavage domain.
 10. Aeukaryotic expression construct comprising the nucleic acid of claim 1,operably linked to at least one expression control element permittinggene expression in eukaryotic cells.
 11. The construct of claim 10,wherein at least one expression control element is inducible.
 12. Theconstruct of claim 10, wherein at least one expression control elementis tissue-specific.
 13. The construct of claim 10, wherein at least oneexpression control element is cell-type-specific.
 14. A method forgenetically engineering cells to express a chimeric protein comprising acleavage domain and a composite nucleic acid-binding region, wherein thecomposite nucleic acid-binding region comprises at least two componentpolypeptide portions which are individually capable of binding specificnucleotide sequences, and wherein the at least two component polypeptideportions: (i) do not occur in the same protein in nature; (ii) do notoccur in the same protein in the order in which they are present in thechimeric protein; or (iii) do not occur in nature with the same spacingthat is present in the chimeric protein; the method comprising: (a)providing an expression construct of claim 10 for directing theexpression in a eukaryotic cell of the chimeric protein; and (b)introducing the expression construct into cells in a manner permittingexpression of the introduced construct in at least a portion of thecells.
 15. The method of claim 14, wherein the cells are in culture. 16.The method of claim 14, wherein the cells are present within anorganism.
 17. The method of claim 16, wherein the organism is a mammal.18. A genetically engineered cell containing and capable of expressing anucleic acid of claim 1.